And when those specialities hit the stratosphere, which they will and quickly, we get to see what a really breaky character can do. Fortunately, limits and hard caps on skill and attributes will put a dent in that. Still, how many best-in-the-world Shadowrunners should be in one team? That and edge will let them blow their limits.
Or for the same price your Sammy can finally buy enough etiquette to not make an assistant of himself in front of Mr.Johnson. Yeah, I'm seeing a problem with this.
Limits are based on stats, which are also relatively cheap to level. But yes, you'll hit hard caps eventually. So you switch over to your second specialty, and max out that. If your campaign lasts a long time, you might get one after that, but probably not. So yes, you probably won't get uberspecialists in
one skill, but you'd get characters which put their points - all their points - in a relatively narrow set of skills.
And yes, your street sammy without etiquette is problematic. But people do that now, with scaling costs. It's
usually not that big problem, since that's what the face is there for, but it might come up at times. It'd still be problematic with the 4 dice he gets from Etiquette 1, but - thanks to the nonscaling system - now most street sams will look at the cost and decide going from "Terrible" to "Bad" for a skill they're unlikely to use isn't worth it. Some people will still take it, of course, if only for roleplaying purposes (sitting out on meeting is boring after all), but it makes it a suboptimal choice.
Which, incidentally, brings me to my second point. This system might work. It needs some balancing pointswise, but as KagedShadow and Xenon point out, it has some benefits. It's not without it's own problems, though, and won't fit any group. If your players just build the character that suits them, it's a simpeler and quicker system which is still more or less balanced. It won't work well with more min/max-inclined players, and for truely long games it'd probably end up being unbalanced regardless. But in the right games, sure.
Kaged, on missions - they're supposed to take about a night, and the karma cost is balanced for that (so about 6 per session, sometimes more). At the start, missions might take longer. Once you get used to the system, the time it'll use will probably go down (especially combat, usually). That does depend on your players, though; some players will go into a lot more detail and that takes more time. So if your players tend to do that and it keeps taking multiple sessions per missions, I'd think about upping the reward (say 4 karma per session minimum, with nuyen equivalently increased). You might as well still give it at the end of the mission though - spending it requires downtime anyway.