ok the Min/Maxer in me is cringing on this one.
First off mystic theurge would very much improve his abilities. If you don't want to loose his cleric levels for rebuke undead and domain abilities you don't have to, just drop 10 levels of wizard, you'll loose 2 wizard bonus feats in return for 10 levels of cleric spell casting. I can see one feat you can easily stand to loose: Combat Casting. Serves no real purpose unless it's the prerequisite for another feat.
Since the players will likely be epic level by this point the low level spells won't matter for the most part.
Spell Compendium is THE book for all your spell needs as it condenses a lot of the best of many other books into one book of nothing but spells.
However in epic levels any non-epic spell pales in comparison to any epic level spell.
BBEG's should be stingy on the Save or Die type spells or even the 'just die' spells (with epic level spells this is easily possible). However Save or Suck spells are fair game and should be used often and lavishly. Go for big impressive spells and try to affect as many PC's as possible, there's on average 4 PCs but only 1 BBEG. While you're at it read the
Evil Overlords Handbook. You're free to make him a ruthless bastard with the common sense to do things right or break every rule in the book and ham it up with cliche after cliche, or somewhere inbetween.
From the PHB:
Time Stop: Yep people just love this one, unless it's someone else using it then they hate it.
Hold Monster mass/Quickened hold person mass: at least 1 or two of the party should make the save and if they all happen to fail have the BBEG spend a round or two gloating or the "explain the master plan" bit that Big Bad Evil Guys like to do for some absurd reason.
Symbol of insanity: any of the symbols are great if the party has no trapfinder or are lax about it, even better if the BBEG happens to be undead or uses the Spell Compendium spell Veil of Undeath he is immune to symbols and doesn't set them off either.
Polymorph any Object: Useful in SO many situations. Create a Spellwarped Half Dragon Half Fiendish Fire Giant for your opponents to play with if you need a second to catch your breath, create a momentary shield in a dome of iron 5 feet thick, fly above your opponents and turn a coin into a 15x15 foot lead brick.
Mind Blank: Do it
Ottos Irresistable Dance: Do it to anyone who doesn't have Mind Blank up. Then laugh.
Sunburst: Blind them ALL, just don't use it when your undead minions are around.
Moment of Prescience: For that time you just HAVE to make the save.
Inflict critical wounds mass: harm your enemies AND heal your undead minions at the same time
Blasphemy: Requires high caster level
Anti-life Shell: keep the good guys away from you.
Forbidance: Block planar travel and hurts people of a different alignment, scatter it around randomly and just walking down a 30 foot hallway can wind up getting zapped 3 or 4 times.
From the spell compendium: Obedient Avalanch, Summon Elemental Monolith (one of the few summons that will give epic level characters a pause), Reaving dispell (great for those that use large numbers of buff spells), Greater Bestow Curse, Maddening whispers