wait and see?
We haven't seen the 3.5 cleric, wizard or sorceror. For all we know, they might get so many new cool class abilities that the MT is underpowered in comparison.
But frankly, I am more interested in the notion that the DMG will have a mechanic in place to create prestige classes. If that is so, maybe we can "reverse engineer" from the MT to figure out how to deal with the multi-class problem with spell-caster/non-spell-caster classes.
1) Take two classes, one spell-caster and one not. Make the prereqs for the new PrC such that one needs to take 3 levels in each of the two classes.
2) For the prestige class, use the worst of the two BAB's, the worst of the 2 saves (for each categories), and the worst of the 2 hd. Use 2 skill points/level, except as indicated below.
3) Now for the hard part -- special abilities. For the spell-caster class, one just adds one spell-casting equivalent per level, it seems. What about the other classes?
Fighter: 1 fighter feat every two levels? (too much? Maybe decrease feats/level or increase prereqs on non-fighter side?
Rogue: 8 skill points/level only OR increase sneak attack damage only (not sure which I favour -- could have different prestige classes for each).
Ranger: (I have no idea until I see the new one)
Monk: Increase unarmed damage only
Barbarian: Increase Rage's only
Bard: Increase bard knowledge only OR increase spell-caster level only.
Paladin: Increase spell-caster level only OR increase Holy Smite only (they are already pretty front-loaded, though)
So how does this look if one mixes and matches? I have not checked whether ANY of the above is balanced -- I am more interested as to whether some of it might provide a clue to solving the multiclass problem.
Of course, then one can raise the same issue with 3 classes, 4 classes, etc. But maybe something similar can be done...
Oh, by the way, if one goes WAAYYYYY! back to the 1st edition Dieties and Demigods, Merlin (of King Arthur Fame) was both a high level Druid and a high level Magic-User, IIRC). So I guess technically, Merlin stands as a possible example of a Mystic Theurge in history. Or at least its Nature loving cousin.

(Saying "Merlin was a druid AND a Magic-User" doesn't work here -- Merlin was beyond that, since he predates D&D, and seemed to have abilities attributable to both sides, while being "unified". Maybe MyT was invented with him in mind?
I think the proof will be in the pudding. When 3.5 comes out, if MyT is too powerful, then DMs should ban it. If it is not too powerful, and becomes popular, than various writers (even Monte. Hell, even John Wick!) will write stuff using them and the writers will either create a niche for the archtype (a la Tinker gnomes, Kender, Gully Dwarves, etc.) or will dig in history and myth to find close matches (a la Merlin, above, just off the top of my head).
Anyhow, this doesn't worry me. In fact, some of my friends probably will go for the idea specifically because it challenges standard class divisions.