GMs, at least by RAW, have the right to disallow characters, or suggest revisions. I don't have a problem with being told my character doesn't work for a game, or needs to be revised to fit the house rules or power level of a specific game. I prefer that to the passive aggressive douchebaggery of some GMs, who allow something, then hit the character with unfair penalties or assorted other crap. You know, the old "Well, if he takes sensitive system, then the corporation is going to forcibly implant 'ware into him when they capture him."
To go back to my earlier example, maybe the GM thinks that things like skin or hair are too easy to fix with simple biomods to be real flaws. I would have preferred to be told this before I started the character, but I could probably adjust to it. So maybe I keep the hair and skin as fluff description, and get the nocturnal quality. At least it's something that fits the character. If the GM simply picked the nocturnal quality for me, I would be more upset, and have second thoughts about the game even if the character wasn't ruined. It's needing to change my character that would bother me, but the choice of how to do so being taken out of my hands.