One idea I'd like to push for in KotC 2 would be more quest rewards like the Chalice quest reward in KotC, as well as more unique items with powers or abilities which can't be enchanted into a regular item.
Almost every single piece of equipment for my party came from item enchantment after 5th level. By the end of the Slavers section, everyone in the group had +3 cloaks of resistance (or a CoD for the wizard), +6 stat boost items for their primary stats and weapons and armor in the +5 total enchantment range. The rest of the game, my equipment kept well ahead of the best loot that we were receiving. (I might add that I finished the game with over 2 million GP left, as well.)
I see no way to prevent that from happening, but it does diminish the thrill of getting treasure or quest rewards when that named weapon you just seized is 2-3 enchantment pluses behind your own equipment.
So why not incorporate some powers, effects or bonuses onto magic items which are NOT part of the regular enchantment system? Call them minor artifacts if you want, or simply say that some enchantments have special requirements. If I find Excalibur and it's just a +5 Holy Axiomatic sword, odds are good it's just barely competing with my current equipment. If I find Excalibur and it's a +5 Holy sword that does +2d6 against demons and grants DR 5/--, it becomes special and I'd have to think long and hard about whether to swap it in for my current enchanted equipment, even if my knight is specialized in a different kind of weapon.
3.5 is so modular, you could drop almost any power or ability on an item and make it different from the "regular" enchanted stuff.