and
I don't care about "viability," and I don't think multiclassing needs that kind of fix. What some see as a bug, I see as a feature. If a PC chooses to divide his time between multiple classes, he will- and should- miss out on his class' higher-level abilities. Even...no especially top-level spellcasting. Thus to me, the "Theurge" classes seem to be a bit of a cheat, for lack of a better word. To this day, I haven't played one.
They do miss out (barring early-entry tricks or applying MT advancement to rapid-advancement PrC's such as the Ur-Priest). The Cleric-3/Wizard-3/Mystic Theurge-9 is a 15th level character, casting 6th level spells - when the equivalent Cleric-15 or Wizard-15 would be casting 8th level spells. At Mystic Theurge-10 (character level 16), the MT finally gets 7th level spells, while the pure caster is working on 8th level spells. The Mystic Theurge is generally three class levels (1.5 spell levels) behind; four class levels (2 full spell levels) when using spontaneous base classes such as the Sorcerer or the Favored Soul. They also miss out on Wizard Bonus feats, Clerical turning, familiar advancement, and so on (with exceptions for some of the later hybrid PrC's). It's only when the Mystic Theurge hits 20th level that he FINALLY gets a 9th level spell slot - and that's only in one of the two classes (MT is only 10 levels). Spontaneous caster base classes don't get 9th level spells with a Mystic Theurge until epic levels.
Those classes also seem unimaginative to me- designed for the purely mechanical reason of appeasing those who dislike what multiclassing does to spellcasters. Coupled with the "Practiced _____________" feats, there is almost no downside to multiclassing a spellcaster.
Reduced spell access hurts (it really, really bites when the divine caster in the party doesn't have the ability to prepare the "day after" spell to fix the penalties from the ability-drain monsters you ran across the day before), and feats are fairly valuable because you get so few of them.
Also, it's mostly only the initial hybrid PrC's that were as vanilla as you're claiming here - the Arcane Hierophant (Druid/Arcanist), Fochlucan Lyrist (Druid/Rogue/Bard mix), Green Whisperer (Druid/Bard), Ultimate Magus (Wizard/Sorcerer), Abjurant Champion (melee/arcanist, although it's possible for a pure caster to eventually qualify), Arcane Trickster (Wizard/Rogue), and so on do gain actual class abilities that often involve mixing aspects of the two base classes.
I'm not saying this is "badwrongfun," just that it isn't to my taste. I understand that multiclassing without the Theurge classes could present logistical challenges to both partymates and DMs alike.
Still, whose business is it if I wish to play a Wiz8/Clc8? Its my PC, and I'm probably running him that way for a reason. If this is an issue with the other players, the player with the multiclassed PC could find a way to carry his weight more, or find a game with players who don't care what someone else is playing.
... except that we're not talking about your PC - we're talking about the PrC's that "ought" to be included in Core. It's not a matter of "whose business is it if I wish to play a Wiz8/Clc8?" it's closer to a matter of "should the Mystic Theurge, and other dual-progression classes, be permitted?"
It's HARD to build a fully split character (Wizard-8/Cleric-8, to use your listing) that can keep up with a pure-classed caster one or two levels lower in total ECL (e.g., a Cleric-14 or a Wizard-14). Other than ones that use really cheesy tricks, I honestly do not think I've ever seen a build that could. Can you make one?
The Geomancer, OTOH, does things few other PrCls do. It introduces new mechanics- Drift. (I like Drift so much, I use it for my hombrewed Fey hybrids...and it stacks w/Geomancer's Drift.) It changes the PC in ways mere multiclassing cannot. Notably, it also allows the PC to mix his class abilities in ways that are most advantageous to him, like armored spellcasting.
The Geomancer isn't really a hybrid PrC - it requires both arcane and divine spells, but it only advances one side of them on any given level.
Imagine if the "Theurge" classes had been designed that way- the Mystic would ignore ASF for certain spells. The Cerebromancer could use Psi points to power spells. The Eldritch Theurge might be able to deliver certain spells with his blast. And so forth. While denied the pinnacle of power that their solo-classed bretheren achieve, they would instead learn exotic techniques and achieve flexibility that their more focused colleagues would envy.
Most of them do that sort of thing - they ARE behind on the pinnacle of power (generally by 1.5 spell levels), and other than the base hybrids in the DMG, most of them do get "mix" abilities to some degree or another.
Or, to put it another way, as nearly as I can tell, most of your objections don't really apply at all, and the ones that do only apply to a relative handful of the hybrid PrC's.