Not good at delineating these things, but here goes a try.
1) If it's in a published source book, and it's within whatever restrictions on availability set forth in the main book, it's available. (No using personal bias to 'knee-jerk ban' something, basically.)
2) If something is presented as an archetype on it's own, consider it it's own thing. (Want to play an Adept? Play an Adept. Want to play a Street Sam? Play a Street Sam. This goes into the whole Augmented Adept thing, as an A.A. is some weird hybrid between the two, IMO.)
3) The PCs should be exceptional compared to others in the setting. I find it incredibly boring to play the 'average person', being rather average, if not a little below, myself, I don't enjoy being that way in game.
4) The GM should build adventures/runs/whatever according to what the PCs can do, whether it's "realistic" or not. Incorporating a lot of scenes in which no PC has the skill to accomplish is, IMO, trying to force specific ways of building on one's players.
5) Backgrounds can be important, yes, but they should not be required. If a player does provide a very intensive background complete with goals which can make a campaign, then it should be used and not ignored. Ignoring such things just makes one think 'what's the point' in the future.
6) If the players make characters with high dice pools, do not increase the dice pools of the opposition over-much. This just leads to an 'arms race' between players and GM.
7) If a PC spends Edge, do not immediately spend Edge with the NPC being attacked to 'counter' the PC's Edge. This just makes Edge even more worthless. On a similar note, NPCs should have a very minimal shared pool of Edge (perhaps 2 or 3 points shared among ALL non-critical NPCs in a session).