You know what? Screw that. Make things intentionally imbalanced on a build point perspective, but then lump additional responsibilities on the 'better' characters. Let the players know that and turn them loose with whatever build they want. Then take the worst offender, straight out of character creation and have him promoted out of the team.
When they complain, and they will, ask them where it says life plays fair.
This does another excellent job of illustrating GMing 101: Don't be a kid with a magnifying glass. Here's the skinny, and listen up everyone.
The reason you want to make things fair and balanced, having everyone use the same rules and be subjected to the same scrutiny and be damned sure that you don't have to veto things, is because slapping players down and tricking them into slipping up is not what the game is about. If you have to slap someone down, it isn't the fun part for you, it isn't the fun part for him, and really, it just makes the whole damn exercise feel more like work then what i like to do on my days off.
Any roleplaying game is about every party involved having fun. When it comes to a GM, I find the best ones are the ones who want to tell a good story and have a good time with some mates. Not the ones who can surprise us with a TPK courtesy of an aerial drone raid because the kid who saw a masked figure 500 meters away happened to be Errant's son, or who gets my gunslinger killed in a quickdraw duel for assuming he's the best, when he has a 22 dicepool for his revolver.
I think players should be allowed to be the best at things, not just arbitrarily one-upped because you think they're fishy. This brings me back to the Power Value. With karma, it isn't that you're less able to be good at things, since you're just as able to excel under both systems, it's that that rating 7 skill costs a lot more then 7 rating one skills, which means he sacrificed a huge number of lower ranking skills just to be damned good at that one thing.
Definitely allow Initiation and Submersion. Submersion is my favourite, allowing me to take a technomancer, and make him into a gunslinger who can also be one hell of a bad ass!