My 2 cents:
IMO, the biggest balance problem with the MT is that it is too weak at lower levels. Play a clr1 or wiz1 and work up to a wiz3/clr3 in a regular campaign. Go ahead, I dare you.
If your party is large, and your focus is not on combat, you'll do ok, but mostly you'll weaken the party until you gain at least a couple of MT levels and start casting 3rd level spells. And even then, not being able to penetrate spell resistance and not having decent spell save DCs is going to hurt. And you won't be casting spells of a level comparable to any single-classed casters.
But hey, bards aren't combat machines, and they have a place in the game, so being weak at lower levels as a clr/wiz doesn't invalidate the character concept, if you're really interested in playing a devout wizard. Giving up power to gain flexibility is one of those choices many players make because it is fun for them. And another publisher pointed out to me that it might be a good option for players who didn't really want to play a cleric but was doing so to cover the healing.
As far as the prestige class having no flavor...devout wizards have flavor already. However, I agree that the class description could have more to it. If it were a campaign specific class with more background material, it would be more interesting. And that's what they should have done..make it an FR class with more background, and still put it in the DMG, like the Red Wizard.
It does irritate me that they can get 9th level spells by taking more levels of one spellcasting class than the other. I think that opens up too many doors to abuse, and it doesn't jive with what little flavor they have. In my opinion, they should take equal levels of both classes, so I've added the following to their requirements for my campaign:
"Your arcane and divine spellcasting classes must be within one level of each other. Gaining two levels more than the other causes a mystic theurge to lose all benefits of the class until this mystical balance is regained."
I like the mystic theurge because it gives my players an option they wanted that they didn't have. I have a player with a cleric of a god of magic who has been trying to figure out how to take levels of wizard without weakening the party. Now he has a viable option. I would have liked the class more if it didn't encourage taking more wizard levels than cleric levels, and if you didn't have to play a weak character for so long before qualifying for it.
It may not be perfectly balanced, but I think it's in the ballpark. My guess is that it's weak at low level, and somewhat abusable at high levels. Time will tell. But my guess is that after the class is out for a year or so we'll find out that:
- Many people who intended to take the class in a regular campaign never went through with it.
- Many people who test the class in one-shot adventures find it to be broken with their min/maxed characters, especially at higher levels.
- The few people who take the class in a long running campaign will find it to be satisfying at higher levels, but only after suffering for a long time.