While a lot of feats are in need of a powerup, I'm not sure the Races of War style feats are the right way to go about it for this project. A lot of the stuff Frank and K talk about in their writeup doesn't apply to E6 at all (only 7 feats ever), while some other stuff is even more important than in 20-level Tome games (nearly all characters are going to be played while between levels 3 and 5, so your first two feats need to define your character in that range). I'd kill off all the stupid feat taxes (every archer needs to take Point Blank Shot at level 1) and either remove or buff dodge, weapon focus, and the like.
You bring up some good points, but one problem; all of the E6 games I've played have been starting at level one and working their way up, and one is still running into the epics. So 3-5 is not the range you have to worry about, it's 1-6+.