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There's not much new analysis needed; we've had the mystic theurge to kick around for ten years. The basic lesson of MT analysis is that caster level and high-level slots are persistently better than "versatile" low-level slots with lower caster level. Any MT build is automatically a worse spellcaster than a pure build of the better of its two caster classes. What keeps the MT out of the "never" bin is that full-progression spellcasting is good enough at high levels that you can still have a viable MT character built around a full-progression class.
So, MT-centered paladin, ranger, and inquisitor combinations with 3/4 BAB arcane classes are consistently, persistently inferior to the 3/4 BAB arcane classes alone, which have better spellcasting before you go into the better class features and equal or better BAB.
MT-centered paladin and ranger combinations with full arcane casters could be viable since they're built on the base of a full-progression caster, but they are completely crushed by deliberate Eldritch Knight/Arcane Archer types of builds. There just isn't enough paladin/ranger spell power to justify any significant degree of MT when you could take full-BAB levels that also level your arcane spellcasting. If you're replacing some pure wizard advancement with MT near the top end in a EK build, okay, but it's minor filler.
Any combinations of 3/4 BAB divine class and a full arcane caster winds up with lousy BAB and HP, because that's what arcane and MT classes bring to the table. They can be mighty casters, but they shouldn't use weapons against anything with a CR in the neighborhood of their level.
Full divine caster MT combinations with 3/4 BAB arcane classes can be viable, though they start behind the 3/4 BAB progression. Holy Vindicator can fill in to boost that BAB; that puts you further behind in cleric spellcasting, but cleric spellcasting is good enough the result might come ahead of a 6-level caster anyway. If you want a "fighter/mage/cleric", a magus/cleric/holy vindicator/mystic theurge can scratch that itch and not be a total write-off. But it'll be a pain to build.