Here is my analysis of the MT:
-By sacrificing higher level spells from a single caster, he gains a lot of lower level spells of 2 classes. Thus, versatility in exchange of power.
-This transaction comes at a price: the MT also forfeits all the other bonuses from both the cleric and wizard (or whatever classes he used, be it sorcerer and favored soul). Those bonus are a steep price: no more casting in armor, no more school power, ineffective channel positive energy, debuffed familiar.
-The MT is very unlikely to ever use up all his spells in a day. First, because the number of rounds in a combat is limited and the encounter will normally end before the MT uses everything (don't forget that the game is designed for 3-4 encounters before everyone is restored to full power). Second, if there is another spellcaster in the group, the group will most likely rest when that other spellcaster runs out of juice, which WILL be before the MT.
Therefore, I strongly disagree with the ones who say that the enhanced versatility compensates the loss in raw power. It may be true in a purely spellcasting point of view, but the sacrifice of the MT goes beyond higher level spells. Plus, he won't be using all the extra powers (in the form of more lower level spells) he received because of the limited opportunities to use them (before everything is restored).
So, what do we do with a great concept, but a class that leads to too many low-level powers and not enough high-level ones? We combine them! I believe that Paizo had a great idea with their "spell synthesis", but that a one-time super-extra-cool-deadly move isn't enough.
My solution is the creation of the class feature "Combine Metamagic". Here is the first draft, comments and options will follow.
Combine Metamagic (Su) A Mystic Theurge may spontaneously apply any metamagic feat he knows to a spell he is casting by sacrificing a prepared spell (or spell slot use for sorcerers) of the other spellcasting class he possess. The level of the spell sacrificed must be the same as the enhancement level of the metamagic feat applied. Doing so augments the casting time as follow: from free to swift, to move, to standard, to full-round, to an extra-full round action (as normal per SRD when a sorcerer applies metamagic). Example 1: a MT uses Combine Extend to cast the wizard spell "fly, swif" as a move action (instead of swift) to grand himself fly for 2 rounds (instead of 1), by sacrificing the first level cleric spell "bless". Example 2: a MT uses Combine Maximize to cast "cure critical wound" to heal a touched ally by 32 + caster lvl hit points. Doing so is a full-round action and he looses a prepared fireball.
Suggestions for game balance: As is written, I think it is too powerful. To limit this, maybe we can assign specific metamagic feats to the MT as he gains level (ex: he can use silent at level 1, extend at level 3, maximize at level 5, quicken at level 9). Or we could limit the use of Combine Metamagic to a number of times per day, that number of times might also be indexed to his class level (ex: once per day for every 3 MT levels). Last, which is my favourite way, have the level of spell sacrificed indexed to the MT level (ex: the sacrificed spell level cannot exceed one half his MT level, round down). Thus delaying the use of stronger metamagic for higher MT levels.