When I make mooks, I keep things relatively simple enough because Shadowrun can get a bit crunchy in the rules. All of them will have generally the same basic stats, gear and weapons, unless I want something special. To that end, what I do for every faction that I run is determine who they are, what kind of equipment and weapons they'd have, and the most important question - how easy do I want these guys to die?
For example, in my Shadowrun PDX campaign, I have various gangs and organized crime elements, notoriously the Red Lotus Triads out of Vancouver (Washington, not BC). Their general go-to mooks are not "Numbered" mooks, meaning they're just gang-bangers who want a job, so they're going to be relatively lightly armed, very few, if any, will have armor, and they'll have vehicles as they need to get around. (In a Triad, mid-to-high level operatives will have a number attached to them, a three digit number based on Chinese numerology that indicates their destiny, and their relative importance in the Triad.) They will be either humans or orks, and if I throw in a dwarf or an elf, they're likely going to be specialized people. Trolls are especially rare in the PDX area, so if there's a Troll among them, he's a heavy hitter, likely leading the group.
Most general mooks at this level are not especially courageous. If the PCs show much force against them, especially magic, they will run for their lives. If even one of them goes down, either hurt or killed, they will run for their lives. This is important because you don't want to make your mooks fanatics unless there is someone there to keep them around, by force if necessary. I usually like to throw general street-level mooks at my players so that they can feel their oats, so to speak, because players love to know what they're capable of.
In combat, mooks like to use cover. They will grab it the instant a gun goes off. And then they will put distance between the shooters and themselves as much as they can, if they can. Savvy players know when and where to choose their fights, so if they're not ambushed, it's likely that they'll choose places where the mooks won't get much cover. Ambushes, in my games, don't last beyond three or four combat rounds.
Now, if you're talking about corporate, government, or higher level syndicate enemies, they may be a bit more capable. Depending on what you want, here's my general rule of thumb for generic baddies:
1) Street Level Gutter Trash: These guys are your typical gangers and hoodlums. They're young, and generally at the bottom of the totem pole. They're often hired as street muscle to patrol and defend turf, to harass people, or to just be a guard for their employer. They will be typically armed with a knife, a pistol, or a shotgun, and maybe one out of ten of them will have an SMG or an Assault Rifle. None of them will have a Firearms or Pistol rating higher than 3. One out of five might have some armor, but nothing fancy. None of them will have magic or cyberware, because that's expensive. If you throw an Ork or a Troll among them, likely they'll be in charge by virtue of their strength and girth alone. But, even those guys will run at the first sign of serious opposition, because getting hurt is expensive, and likely they won't have the DocWagon contract to help them out, so they'll run. They like fights where the odds are squarely in their favor.
2) Made-Men/Gang Leaders/Corporate Security: Okay, these guys are just a few notches above the trash. They'll have the weapons and gear necessary to do whatever job they need to have done, but unless they're working full-time in security, they don't always wear armor. It is important to be frugal in the gear and cyber department, because while they're better equipped than street trash, money is still an object, so don't outfit them with the best stuff if there isn't any cause to have it. They may have cyberware and may have a mage on their teams. They won't run until it seems they're overpowered in some way, or unless they've got specific instructions on what to do in case a fight breaks out. Corporate security, for example, when encountering a shadowrun team, will always have someone communicate with others to the threat, and maybe even call in local law enforcement if they know they don't have enough to handle the situation. They are not stupid, but they're likely not going to risk their lives for something when the cards are not in their favor.
3) Shadowrunners/Mercs/Soldiers/Heavies: Now we're talking. You have to really think about these guys for a bit, because they're not stupid and the objective is keenly in their minds at all times. They will be prepared for your players, unless somehow the players are at an advantage,which you'll have to figure out. They can be as fanatical as you'd like, but always consider that they will retreat if that's the best option. Magic is almost a certainty, but you've got a lot of wiggle room to make whatever you need for your situation.
4) Elites: Anything goes.
