Spell resistance
I would like to have seen a spell that allows arcane casters to give themselves Spell Resistance, and perhaps a chain of feats that allow casters to increase their ability to defeat SR. There is spell penetration and greater spell penetration, but I have been told that these feats will only grant a +1/+2 bonus rather than the +2/+4 they used to grant. (I don't have the books yet) So, for casters, everything seems to have become more difficult.
While the books compare SR to AC versus magic, it's not a true comparison, because when a fighter swings his sword and misses the target, the fighter still has his weapon in hand and can attack again, but when a caster fails to beat spell resistance, the spell is gone. This makes the caster less reliable and the players don't feel like they are able to contribute in combat encounters.
Even in 3.0, at high levels, creature SR's in the low to mid 30's cause casters to lose 50% or more of their spells if they cast them on an opponent. For instance, my 17th level wizard with greater spell penetration gains a bonus of +21 to overcome SR. Unfortunately he no longer faces opponents with SR 21 to 25. The opponents he's been coming across have SR's of 31 to 35. I have to roll a 10 or better just so that my spell has a chance of working. Roughly 50 percent of my spells, cast on enemies, fail. Even if the spell succeeds, there are still resistances, immunities and saving throws to overcome. When you start wasting 6th, 7th and 8th level spells on one enemy, you've wasted a lot of fire power, and thus in succeeding encounters, the wizard is less likely to play a significant factor.
In 3.5, if what I have been told about spell penetration is true, then my wizard only gets a +19 added to the die roll to beat SR. A creature with an average SR of 33 will require a roll of 14 to beat, and thus the wizard's spells will fail 70 percent of the time. The end result is that my wizard will spend more time buffing, (oh wait, those new durations of 1 minute per level make the animal buff line of spells much less attractive, so they probably won't get memorized) waiting to teleport the group out in case of an emergency, and being a target. He'll probably have "Dispel Magic" and "Greater Dispelling" occupying almost every slot so that he can be strictly reactionary in combat situations. In the end, it's probably time to tuck the spell book in a Leomund's secret chest and start a new fighter.