Vicar In A Tutu said:- Magic (buffs, some overly complicated spells, polymorph spells are a nightmare)
- Skills (creating a high level NPC takes an insane amount of time)
- Grappling rules
- High level characters becoming demigods (it feels like I'm playing a different game at higher levels)
Magic - simply disallow all the spells you don't like. You should eliminate similar monster Spell like abilities.
Grappling - compared to other bits of 3e I don't find it that complex, sorry. Maybe reduce the size bonus to a +4 if you're larger than opponent, I'd say that was plenty.
High level demigods - maybe cap item '+' at +5 rather than 'virtual +10', half the rate of XP gain, and tweak NPC demographics so 20th levellers really _are_ demigods, and go back to OD&D's spell level cap of 6th; it's the 7th-9th spells that cause most of the problems IMO.
As far as NPC demographics go, having baseline NPCs at ca 3rd level instead of 1st, and the top guys at ca 12th instead of 20th. This creates a much more stable campaign world where armies actually matter - a 12th level Wizard can destroy a battalion, but not a division (IME).