For arguments sake: lets assume 2 runs a month. If the average payout per character is $5,000 and 5 karma.
At the end of a year characters have made:
$ 120,000
120 karma.
Which is a fair bit of both. Cash characters have to be economical in their purchases but can get some nice stuff with their cash. The Karma can go towards improving their weaker areas and strengthening their primary skills. For Karma based characters, the 120 karma with mostly go towards increasing their primary stats (Res and Magic) and towards their primary skills, making it a toss up for shoring up a weak point, or improving a primary skill. While the money is nice, it will mostly go towards lesser useful items (lifestyle, clothing, reagents,) things that don't really augment their abilites (with the exception of the Face)
You also have to consider the costs of shadowrunning. During 12 months, you've spent 24,000 on low lifestyle or 60,000 (half of what you've made) for medium. What about bribes, ammunition, replacing gear, or burning SINs? What if they get double-crossed, make a moral choice, or do the run as a favor to a contact and get no pay? None of that over the course of an entire year? I'd also say that with the price of decks and cyber, 120k won't get you as much as 120 karma. It's also a pretty decent amount of money. Even doubling it makes it difficult to explain why the characters would be risking their lives twice per month.
I would like to see an attempt at making rules follow through on the fluff of characters getting paid in favors, stock, corp script, equipment, and other illiquid assets. You can't pay rent (at least not as easily) with those, but you can improve characters that way. Plus, it's a good way for Johnsons and Fixers to lock the runners they've invested in into the lifestyle of running. Maybe a better lifestyle lets you launder more money, so there is a mechanical benefit to the higher lifestyles.
Without that figure the costs and lifestyle, and go for the players netting (not grossing) 2,000 nuyen per karma?
First off, a GM shouldn't be a dick.
Yes you will get screwed sometimes, but the trend should be a move up in pay as the team encounters harder and harder missions. Not throwing the players in a meat grinder then stealing their pay or backstabbing them at the last minute. Every time. Sure, it can and will happen but it shouldn't be every time, and we both know (as players AND GMs) that the characters aren't going to let that stand...
TBH, usually the only time I screw over my players (shall we say) is when 1 of 3 things happen:
1: they screwed up, and thus fon't desirve the pay.
2: when it's a lead in to an other mission (wich usually results in them recovering their pay plus "something extra" - usually something good. Like a new deck, or drone, weapon, etc)
3: when its a "plot element" - and they usually get compensation some other way..... just not direct cash. (Coffee beans, fresh fruit, important contacts, favors, allies, and clout are samples)
And, as wyrm pointed out, some corps like to pay with goods. As do the underworld. Drugs, weapons, slaves, and even cyber/bioware tight down to foci are all things that various underworld johnsons like to pay with.
Don't get me wrong. I am not saying that Runners should only be making "$2 -5k a run forever". I am saying that the pay fits the reputation, threat, and skill level of both the Runners and the mission. As their skills and Rep grow, they get harder runs, which in turn leads to more pay per run. The issue i think, is that starting point and value of the runner.
A fresh character is assumed to have "cut their teeth" and survived at least their pro-am days. (Wouldn't know it from some builds i have seen... but yea.) BUT, they have no rep in the shadows (kinda a disconnect but hey,) so there is NOTHING that sets them appart from anyone else in the runner community - yet.
Once you fill that "yet", you pay hoes up or down with your rep (be it goid or bad.)
Basically, if you want to be paid big bucks, you have to prove it. Again and again and again. And then you get the big bucks.
(But yes, a nice GM should throw the characters a bone sometimes too. Throw in a deck upgrade, foci, cyber/bio enchancement for an exceptional job done! As "Iduno" pointed out some fixers and johnsons like stables (even if the players don't think of themselves as kept) and really, alpha wired reflexes 2 doesn't cost EVO the price they charge you.... and it will make that sammy a little more likely to take the next job that needs done too, possibly even cutting out the "Fixer" side, saving the johnson down the road...)