My thoughts:
1) One solution to the dragon spell-battery problem is that posed by Monte Cook in an online article a few weeks back:
http://www.montecook.com/cgi-bin/page.cgi?otherd20_Spellcasters
This is also a philosophy that informs my current game: Switching to Iron Heroes rules and to a spellcasting class with lots of constant "buffs" and a limited array of fire-and-forget spell effects. Doing this with monsters like dragons would seem to make sense as well: Just give them an array of always-on effects, protect them from the typical nuke spells that get thrown around at high levels, and let them have sufficient spell-like abilities to pull off the big-gun tactics (scrying, teleporting, etc.).
2) Simplifying bonus and penalty types would definitely be a step in the right direction. As it stands, there are simply too many different kinds of buffs and debuffs in the game. Streamlining them would seem to make sense. While I understand it might detract
slightly from the "rules mastery" effect, I think it's probably a worthwhile tradeoff.
3) It seems to me that a lot of the "complexity" in 3e is due to the fact that feats, spells, items, and classes are now spread across a vast number of supplements, and especially the fact that designers have kept adding new options to fill in gaps that they see in the core rules. For instance, a unified spell list plus the ability to combine caster level and spells per day from multiple spellcasting classes plus pushing some class-defining spell effects into the realm of class abilities would radically reduce the need for mystic theurges, geomancers, the Arcane Disciple feat, et cetera. Likewise, making fighter/mages more workable in the core itself could obviate the need for the bladesinger, duskblade, eldritch knight, spellsword, etc.
All of these issues might well be comfortably and simply resolved by a (gulp) fourth edition. For instance, there's no reason why one couldn't just have written Quicken Spell to lower a spell's casting time by 1 action or action step, as in Arcana Evolved. That would have obviated the need for Dave to be looking through his own book for the appropriate feat (that's Rapid Spell, Dave).