How much do you intend to support league play and the habit of players effecting the meta game.
Bunnyhopping for example. It was for the best taking it away from marines in that ns1 patch but I think it still took some persuasion from the community to convince you to keep it active for aliens which saved a large skill curve from being removed especially for the skulk.
Cvars, a big disappointment for clanners nerf wise when you locked things like r_drawviewmodel and the muzzleflashes. Despite these being an option for everyone and also being known by everyone who cared a whit about playing competitively you decided it was unfair if even a minority players (who by extension cared the least) out of thousands were unaware of cvars so you took them away from everyone to spare a few green people the possibility of playing in ignorance rather than letting them learn the in's and out's of common first person shooter config'ing like most people do in most other games. (Am I still bitter after all these years? :/)
New things that are discovered that arent obviously broken or blatantly exploitative. When new quirks and tricks are discovered there's always a segment that believes its wrong for various misguided reasons (not part of the developers vision is a tired classic) or they simply haven't learnt how to do it yet and therefore campaign to get it nerfed or removed.