Per Rest Period mechanics. I'm not going to call them 'per day,' because the typical PC's workday is about 10 minutes long. It's not the Vancian magic I mind, so much, it's the fight-rest-fight cycle and the assumption of attrition. Vance's spellcasters needed have time to re-memorize their (very few and very powerful) spells, and they were limited by the time and concentration that took and often the lack of portability of their spells - not by 'days,' by which I mean how often they got a good night's sleep. Also, they didn't completely suck when out of spells.
Armor Class and Saves. Saga's Defenses system has completely soured me on these being separate concepts. At least this is really easy to houserule.
Alignment as a mechanic in its current form. Pretty obvious, I think.
Mechanics for enforcing a particular class/race combination, aside from making characters of certain races mechanically well suited for certain classes. Dwarven wizards being more sensible than elven wizards in 3e being a glaring example of the inverse.
A dichotomy between 'PC races' and 'monster races' based on which ones were in the Fellowship of the Ring. Obvious.
Magic item dependency. A relatively young sacred cow, but already ripe for the slaughter. Make magic items magical and RARE and COOL, not +x to y required to not die.
Gameplay death and resurrection as default assumptions. My Gamist side doesn't need them to feel challenged, and they sure as heck don't represent the source material. Death should be dramatic, death should be either agreed upon or due to resource expenditure, and death should be FINAL except for artifacts.
Spell levels. I'd rather they be CALLED something different, but either remove them or make them synch up with character levels.
The Great Wheel and the Planescape outsiders. These are fine - for the Planescape Campaign Setting release in 2010 or 2011. In the meantime, give me more generically useful demons (console RPG style weird ancient evils) and devils (medieval style sinister manipulative hellspawn) and angels (holy, radiant beings of light).