Here is a list of simple seed ideas that I wrote out a long long time ago:
1. Babysitter - Protect rich kid Brat Johnny G while he goes out on the town for a night.
2. Hostage Negotiation/Retrieval - Negotiate the release of/Retrieve a/several VIPs.
3. Anarchy - Create one hell of a distraction
4. Test Run - Test a new corporate HQs security systems (of course they don't have to tell you what's going on

)
5. Metal - Play security to a street concert for an up and coming metal band.
6. Infestation - Clear out an infested research facility and save/eliminate key personnel.
7. Yakkity Yak - Dress up as Yak hitters and take out a few specific mobsters quick. Then dress up as mobster and take out some Yak and Triad indiscriminately.
8. Prizefighter - Ensure that the crowd favorite does not win the next match.
9. The Beast - Accompany a reknown big game hunter and protect him from threats as he delves into the awakened forest to take down the world's largest recorded awakened crocodile...with a bowie knife.
10. Zoology - Steal an awakened tiger from the city zoo.
11. Flight 187 - Extract a target from an international flight.
12. Khan - Take out a ganger trying to unify the cities gangs and frame several of the gangs for it to spark doubt on the alliance.
13. The Frame Up - Frame a guilty man for the crime he managed to succesfully cover up.
14. Cold Blood - Investigate a brutal murder so that he victim's family can take care of the murder before the law catches up.
15. Vigilante X - Discover the identity of a vigilante that has been trying to save the town.
16. Late Johnson - Survive being framed for murder when you're caught at the meet sight and a later Johnson drops in from above. (Had the Johnson thrown from a roof and land at the group's feet as they were entering the building when I did it)
17. Jailbreak - Bust a known (and deserved) felon out of MaxSec for the Johnson and get him to international waters
18. Art Burn - Break into the city museum and destroy several pieces of art.
19. The Package - Deliver a package from Seattle to Hong Kong and fend of the bizzare crowd trying to obtain it. (Package should be something really out their like the newest prototype of the Studmaster 3000...ya you know you liked the pun.)
20. Pan-Galactic - Play club security for VIP record producer Mason Maxwell at the hottest club in town.
21. High Yield - Steal a very "hot" delivery coming into the city and deliver it to the Johnson while evading Homeland Security.
22. Elemental Rock - Defend an old rocker that left the biz from his deranged and pissed ex-band mates. Oh and their all shamans.
23. Mall Rats - Break into the mall on Thanksgiving and still the Black Friday shipment of 2072 Rock Me Dunkie.
24. Field Trip - Kidnap a CEO's son from a school field trip to a theme park. (Cue beverly hills cop music)
25. Field Test - Field test the newest project for the Johnson and deliver it back undamaged with the test results. May include protecting a scientist during the testing phase.
26. Pirates - Protect a cruise liner from a pirate attack that the Johnson knows is coming.
27. Fatal Extraction - Extract a target and make sure that they die during the extraction. Must return with the corpse.
28. Launch Failure - Make the renewal of the space projects first launch an utter disaster.
29. Interception - Intercept a group that is trying to steal a package from the Johnson and make sure they learn their lesson.
30. Wise Man - Rescue an old wise man from an village under control by an African warlord tyrant.
31. 8 Heads - Deliver the heads of eight men to the Johnson. (He provides a duffel bag for storage

)
32. Driver - Play get away driver/extraction team for a group of Prime Runners in town for the evening.
33. Recipe - KFC is remoddeling their security vault. Steal the recipe for the special blend of herbs and spices while it's being moved around in an armored enclave with heavy security on site.
34. Tin Man - Disable and return a rogue cyborg.
35. Advertising Principles - Create an advertisement for the new Predator Vs good qualities by using it to assassinate one of Colt's lead R&D scientists. Advertising is money friend. Recommend not getting face shots during the filming.
36. Gang Violence - Brutalize eight gangs in the city to reduce the rising gang numbers. Preferably set them at each others throats over territories in the barrens.
37. Fire Sale - Disable the city's electricity, water, and matrix service.
38. Super Jet - Steal the plans for a revolutionary new plan back from a company that stole it from the Johnson...or did they. (Shamelessly stolen from the first episode of leverage)
39. Fort Night - Break into a military fort to...deliver a message to a man in on site lockup.
40. Expendable Heroes - E-X-P...E-N-D...A-B-L-E-S, expendables, expendables (sung to the mickey mouse song tune). The group is hired to assault a low security (according to the Johnson) compound and severely damage it's infrastructure. Of course it's just a distraction for the real job.
41. The Clerk - He wasn't even supposed to be there today, but he actually came into work when the boss called him on his day off. It could ruin everything. Get him out of the building by any means necessary.
42. Block Buster - Kidnap block buster starlette Kim Heights for the night. Deliver her to her apartment unharmed, but in appropriately tattered and stylish garments, the next morning.
43. Beer Run - Smuggle a few hundred cases of Cascade Tempo Ale into Seattle for a bachelor party of the century.
44. Mail Man - Steal a package out for delivery.
45. Subject 5.2 - Break into a facility and extract subject 5.2 from cell 9. (Subject 5.2 is a very horny red ape, and the Johnson does not mention specifics unless grilled for them)
46. ED 209 - Disable a damage heavy combat drone that is rampaging through the city and plant the bodies of a militant group at the scene after removing the drone.
47. Deployment - Spark a skirmish in Africa to ensure that active soldiers are deployed at a low staffed nearby base.
48. Treason - Deliver a rifle to a certain point in the city that is restricted access without being noticed by secret service security teams.
49. Secret Secret Service - Protect the president from an assassination attempt without his, or the secret service's, knowledge.
50. Action Heroes - Eliminate a group of gangers that have taken bloody hold of the Plastic Jungle...while on camera for stock footage to splice into this summer's action title
Blood Gore and Mayhem 27: The Last Act Part VIII, One Final Bullet.
51. Central Bank - Take Hostages and keep them in the bank for 48 hours. Do not steal anything. Casualties are acceptable.
52. Have a Heart - Steal a heart being transported for human transplant and get it to the Johnson before it's time is up.
53. Public Execution - Hit a politician during his election parade.
54. Air Force One - Air Force One has gone down over the Cascades, get to the wreckage and obtain the nuclear football before anyone else.
55. Joyhouse - Rescue the Johnson's daughter from a Joyhouse and slaughter all the management linked to the joint...painfully.
56. Game Con - Extract a target from Gen Con 2072.
57. Simulation - Prove that a famous pop star is really just a agent with personality software. (Taken from the movie SimOne)
58. Vat Job - Break into a black clinic and kill a famous street sam while he's in a vat healing from his upgrades.
59. Clone War - Find the source that keeps cloning powerful CEOs and destroy them/their facilities. Unfortunately, the Johnson was an escaped clone trying to destroy those that made him and has no resources to pay for a job well done.
60. Cold Case - Figure out who is after the Johnson and deal with them. Unfortunately, the only leads he has are all related to a case from 2012 and it looks like they'll have to solve it before they can figure out what's going on.
61. Convoy - Guard a convoy on its way from LA to Vegas and protect the cargo containers at all costs. Of course it wouldn't be a good session if a bunch of good for nothing runners didn't try to hijack the cargo.
62. SEAL - Rescue a group of SEALs and hostages from an oil rig that has been taken over by terrorists.
63. An Act of War - Assassinate a head of state and frame a foreign country for it, but not before you plant data files and evidence suggesting secret alliances and active support of the actions all across the world. Will this be the beginning of WWIII or has it already begun?
64. Heavy Metal - A cyborg went dark on an assassination mission in Europe. An alliance was formed with his target twenty minutes after he went dark. Stop him, and do so without bringing attention to his intent/controllers.
65. The Hanging Men - A gang is hanging patrol officers from street lamps all across Seattle. The law is cracking down hard and the national guard is threatening to move in, putting a cramp on the biz. Track down these gangers and make an example of them by hanging them from the security fence at the down town precinct.
66. Death Shroud - Steal an ancient artifact from an Egyptian mummy exhibit and return it to the Johnson. Things go bad after the group takes it. Is it cursed or is this just a complete coincidence?
67. The Holy Grail - A researcher's son went off on his own in the middle east claiming he found the secret to the holy grail's location. He hasn't been heard from in two weeks and the researcher just received a ransom notice. Rescue his son and bring the head of the kidnapper back.
68. Prisoner Transport - Hit a prisoner during his transport from sentencing to MaxSec. Proof of his death must be made available through a public media source (news, youtube, etc.)
69. 2000 rounds - The Johnson provides the runners with an HMG and 2000 AV rounds of ammunition. The job is simple. Destroy as at least half the vehicles in use by Highman Express Shipping. (The Johnson neglects to mention the companies airplanes but will count them when comparing the numbers and cut pay by an appropriate percentage if they weren't dealt with.)
70. Barren Blues - Steal an underground blues singer's music recordings for a record label.
71. Destruction - Destroy a gang's base of operations and disrupt all of their resources. The group must be scattered past being able to regroup.
72. Spy Games - Pursue a target and abduct him during his romantic date. Torture him until he gives up a pass-phrase and then let him barely escape. Tail him to his home/hotel and then call the Johnson. (It's all just an elaborate game set up by a couple thrill seeking high ranking wage slaves.)
73. Sick Leave - Destroy a R&D scientists doctor's notes and plant evidence that he has been faking his illness.
74. Plague Prevention - A biological leak may have occurred at a remote corporate owned lab. Unfortunately for the personnel, they are considered expendable and the corp wants to take no chances. Eliminate the personnel as a precautionary measure. (The leak did occur and is was a virus that makes the subject highly contagious, strong and resistant to pain but dumb as a box of rocks...that's right...pretty much a zombie. If you really want to be blatant have the remote lab be part of a high class mansion.)
75. Seattle's Most Wanted - Get a highly sought criminal out of town without being caught by the police or border patrols. The city is locked down and everyone is on high alert looking for this individual.
76. The Card - Break into a penthouse suite and steal a card that the resident owes the Johnson for a bet that was never paid. Take/Damage nothing else.
77. The Book - Break into the estate of a recently deceased fixer and steal his commlink of contact numbers before it gets unwittingly sold at the estate sale.
78. The Hotel Job - Extract a target from a hotel. Dump a body in the targets room and torch the building while you're at it. (It's all really just a giant insurance scam.)
79. Hit the Hit Team - A high class team has been hired to take out a key politician. Hit them just after they've completed their hit. (The Johnson has another hit team set up to hit the runners. She's really a hitwoman trying to thin out the competition.)
80. Missing Queen - Find a missing CEO that was last reported to be on an African Safari.
81. A Simple Run - Break into a corporate owned warehouse, steal a crate, and deliver it to the Johnson. Get Paid. Everything seems far to easy and flawless. (Make sure to have plenty of perception, logic and random rolls ready to amp up paranoia, but hey...everyone gets an easy one now and then)
82. Cleaning House - Loyalty test a group of corporate citizens by kidnapping them and torturing them for information/bribing them to betray their company. Deal with those that fail.
83. Epidemic - Release a biochemical agent on a terrorist village in south america. Things get complicated when it begins spreading like wildfire.
84. 9...8...7 - Plant a series of explosives around town designed to create the ultimate mix of panic and destruction at ten PM the next day.
85. The Island - Break onto a corporate controlled island and infiltrate their research labs for information on a classified project.
Added a few more from the list.
Having a single Big Bad Wolf-Monster type situation tends to be a poor option for a story, because it works out one of two ways:
I would like to point out that the Big Bad Wolf style of villain does work in the Shadowrun system, it just requires a careful balancing that most GM's just aren't that good at. (It actually works this way in almost all systems when you get down to it)
There are main points to consider when creating an NPC meant to be a combat opponent: Offense and Defense. Making an opponent that is able to stand up against multiple PCs while not butchering them requires an overwhelming defense and a mediocre to average offense.
However, what most GM's come up with is either A.) an overwhelming Offense
and Defense, in which case you end up with:
1) The PCs are utterly helpless and get slaughtered if the GM doesn't asspull something to save them
or B) an overwhelming Offense with a mediocre to average Defense in which case you end up with:
2) Their numerical advantage chews the thing down in a hail of gunfire in seconds, regardless of its abilities.
Of course if the players don't take simple precautions, an mediocre or average fight can put them on their asses (Even high level D&D characters feared my kobolds damn it. Enough pit traps will wear down anyone.)
This isn't just an assumption on my part, but a lot of experience with games that have big bad evil guy fights and are much much much more lethal than SR4A's system (like comparing a switchblade to a flaming chainsaw coated with cyanide). For example, Hell on Earth's BBEGs had a specific weakness to even be capable of killing them, and we aren't talking about weaknesses like silver, insecticide, or clipping them in the heel, we're talking about things like "must use a weapon crafted from a piece of his bomber that he crashed 13 years ago when the bombs fell and buried in the Mojave" for a guy the group is unlikely to every get a conversation out of about his past to find out about said plane.