1) Most games I've been in have just used the average. And imx damage outstrips HP anyway, so maxing out the dice shouldn't be too big an issue (assuming reasonably optimized PCs).
2) Low-level spells as at-will is the obvious. For melee, at-will ToB powers possibly (rewrite the readied/granted tables to acount for it). However, both would have the problem that they weren't designd for it - things like Fabricate as an at-will would be too much, and Emerald Razor at-will would be ridiculously strong. Not sure this can be done without an extensive rewrite. Probably best just to give a bonus reserve feat or two (maybe make em stronger?), but even a weak at-will power means giving something to the most powerful classes in the game. A massive rewrite could be an option - e.g. Wizards get much fewer spell slots, but certain spells have an at-will ability - e.g. if you prepare Fireball you get an at-will fiery burst similar to the reserve feat. It'd be a big task to write a whole new system tho. No idea how to translate it to melee, but they've already got at-will stuff anyway.
3) *shrug* I just give everyone Able Learner for free - streamlines the skill system nicely as it gets rid of cross-class premium and the need to track at which level points were spent on certain skills. Folding them in is easy to do as well.
4) Hard to make this work imo. Push and Pull for small distances (e.g. 1 or 2 squares) is meaningful when shifting is a move action, but in 3.5 with the 5 ft step it's meaningless. Just look at things that move you 5 feet - have you ever seen anyone take the Tiger Claw feat in ToB? Or Pushback from the MinisHB? Best idea I can think of is to change the Massive Damage rules - instead of save vs death, if you exceed the threshold then you get a free bull rush (and don't have to move with them). Large monsters (who deal high damage and have big size mods to bull rush checks) would be very cool, but very deadly, so would probably require a CR increase, and Large PCs just got better (and the Small ones got worse).
5) Ranged touch spells work, normal attacks rolls just won't work in a game of varying BAB progressions, no implement bonuses, etc. You could use "attacker rolls" where everyone basically takes 10 on saves, and the attacker rolls to beat that DC, but imo it opens up more problems than it's worth (mainly, what natural 20s and 1s now mean).