I'm not quite sure how best to respond to this. Has the collective wisdom really reached the stage of thinking 3rd edition was a badly designed game but we on EnWorld might still be able to rescue it into something playable?
Lots of people played it for a very long time, including me. I am still playing it, in as much as I'm still running Pathfinder 1st edition - including at high levels.
The best way not to break the game is to agree that you are not going to break the game. If everyone agrees to that in advance then it's not necessary to have a long list of banned rules. I think the only thing I banned outright was the Black Tentacles spell, and that was because of the sheer tedium of the 3.5 grapple rules when used against large groups (I'm happy to allow it in Pathfinder games since grapple works differently).
Its great strength is that characters are incredibly customisable, so you'll never run out of things to play.
From the DM's side, I think it is important not to be too caught up in the details. All the time spent making sure enemies have the correct number of feats, skill points etc. is time that you could have been spending coming up with awesome situations. And if the PCs are having too easy a time of it, give the monsters the Advanced template from Pathfinder i.e. +4 to all ability scores.