I was also thinking of things like Toughness, which seems like a good idea if you're new, but is really just a trap to punish people who don't have a firm grasp on what's actually good in 3.5.
One change I've tried in the past with Toughness is having it grant +2 HP at each level after first (so, if you took it at 1st level, by 20th level, you would have accumulated +41 HP total). Unfortunately, those games didn't survive long enough to discern if that was a horrible idea or not...
The toughness boost is just a further lure into the trap of a still crappy feat, IMHO. If anything, nerf Toughness to discourage it or go whole hog (maybe let it double your Con bonus every level).
Not every feat is meant to be taken by players. Players don't need the Run feat, they can buy horses. Horses need the run feat. Players don't need Toughness, their hit points aren't so pathetic that +3 makes a difference. Animals in the wild need Toughness. Players don't need Mobility, there are better feats to chose from than wasting two feats to move out of a threatened square with a +4 bonus to AC. NPC pickpockets would need that all the time and wouldn't have use for the better feats.
And quite honestly, when class features and wondrous items regularly grant sub-par bonus feats, does it make sense to upgrade every sub-par feat to super-awesome level?