
UnArcaneElection |

Even before this SLA FAQ nerf of a few weeks ago that made Mystic Theurge essentially useless by preventing early entry, it would be better to have a single-class Cleric and a single class Wizard. Not only would they be stronger at their specific classes per level, but they would also have better action economy, as well as not being a single point of failure (if either one goes down, the other one might be able to come to the rescue -- obviously easier if the Cleric is still standing than if the Wizard is still standing, but the other is still a possibility).
So what you really need to ask is: Would you rather have 1 Mystic Theurge or 1 single-classed arcane/divine hybrid, as indicated below, in 3 categories, depending upon what proportions of arcane and divine you want:
Mostly arcane with a bit of divine:
White Mage Arcanist
Magambyan Arcanist (prestige class and not actually an Arcanist archetype, but has full spellcasting progression from 1 full caster base class, with no interruptions)
Bard (6 level caster, not full caster)
Razmiran Priest Sorcerer and prestige class (also has full spellcasting progression from 1 full caster base class, with no interruptions, but can't really cast divine spells until high level, so has to fake it at lower and middle levels; still just 1 full caster base class)
Spell Sage Wizard
Mostly divine with a bit of arcane:
Ancient Lorekeeper Oracle
Shaman (certain builds? with Lore Spirit and Arcane Enlightenment Hex, possibly approaching full blend? -- need more study)
Officially arcane, but really a full blend of arcane and divine:
Witch (some Patrons more than others, but base Witch spell list already has a pretty good mix)
After the SLA FAQ nerf, any of the above beats Mystic Theurge hands down. But before the SLA FAQ nerf, the answer to this question was not so clear-cut. Any of the above single-class types (or Magambyan Arcanist since this was uninterrupted progression from 1 base class) would have a caster level advantage (including highest levels of usable spells) over Mystic Theurge, but would have less spell diversity for comparison of prepared to prepared or spontaneous to spontaneous, and would have less lower level spells per day. Which one would have more class features other than spellcasting depends upon the particular base class (or prestige class for Magambyan Arcanist or Razmiran Priest) -- the Witch is the champion here (most Hexes are limited only in how many times you can cast them on each target rather than how many total times you can cast them, and Hex Vulnerability even gives a workaround for the former); the Shaman follows behind (has Hexes, but not as many of them); Bard comes after (many abilities, some having limited use quantity, but limit is pretty high); Ancient Lorekeeper Oracle and Sorcerer-based builds come after that (multiple abilities, but many of them have low usage limits); Mystic Theurge comes after that (narrow set of abilities having to do with cross-class casting); Wizard-based builds come last (Arcane School abilities and Bonus Feats are few and far in between).

lemeres |

Two characters.
Setting aside the fact that the Mystic Theurge is terrible, two characters have better action economy.
There is no scenario I can think of where a Mystic Theurge alone is better than two casters. Or even as good as a single one.
It might be better to say 'two mystic theurges vs two different types of caster'.
I can think of scenarios. For the purposes of this discussion, we are going to imagine a 2 on 2 duel between these characters.
Since we are talking about a duel with a handful of casters, obviously, that means a lot of spells, and likely many SoS spells, will be flying about. Obviously, the specialists have an advantage in sheer power.
However, divine casters are typically the ones with healing/status removal. If the mystic theurges target the divine caster, they might remove the other side's ability to remove various conditions. In contrast, if one of the mystic theurges gets hit with a condition, the other can fix the problem.
Specialists have a greater ability to causes conditions, generalists have more versatility that would allow them to deal with the problem.
Of course, with the simple addition of scrolls, you can have the arcane caster handling the occasional condition, which means the scales are far more in their favor. Witches and other non-core options also mess up the scenario.
So...as a hold over from 3.5...it was of somewhat shaky use originally, and now has mostly been made obsolete by new class options that do the blending more thoroughly without so much sacrifice. But you can hardly blame the mystic theurge- it is the product of rather different design doctrines (with 3.5 loving prestige classes, while PF highly encourages single class dedication).
It is much like a penguin- waddling around in our lands, but swimming gracefully enough in the environment it was adapted to.

Wheldrake |

The problem with a mystic theurge is their late access to given spell levels, especially at first. Sure, it's awesome to have both cleric and wizard spells and powers. But it's far better, IMHO, to have the quickest access possible to new spell levels of awesomeness.
Though I'm sure there are tricky ways to make up for some of those lost class levels. I'm eager to see all the ways. If a Wiz3/Cleric3/MT1 could have access to 4th-level wizard spells in addition to all the rest of the awesome cheese... I would definitely change my view on MTs.

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I'd rather have a cleric + a wizard, at any time, any day, having both, would mean that I can customize the cleric list to a ridiculous degree to cover the weaknesses of the duo.
and If i really wanted a spells from the wizard or whatever spell list, of another class, would just play a Samsaran and add them to my spell list.
Yeah I know you can't mix divine and arcane but well, Shaman for examples has a couple of arcane spells in their divine list, so if you wanted to add them to your cleric list, you could. Just like Witch has the cure spells and even heals, so a wizard can add Heal to their spell list with Samsaran mystic past life.

UnArcaneElection |

The problem with a mystic theurge is their late access to given spell levels, especially at first. Sure, it's awesome to have both cleric and wizard spells and powers. But it's far better, IMHO, to have the quickest access possible to new spell levels of awesomeness.
Though I'm sure there are tricky ways to make up for some of those lost class levels. I'm eager to see all the ways. If a Wiz3/Cleric3/MT1 could have access to 4th-level wizard spells in addition to all the rest of the awesome cheese... I would definitely change my view on MTs.
That's what the previous SLA FAQ (before the current nerf SLA FAQ) went part way towards doing. See this awesome guide (unfortunately now obsolete). With the right combination of Spell-Like Abilities, you could be Arcane 2/Divine 1 or Arcane 1/Divine 2 and then start Mystic Theurge, thus not losing more than 2 levels of 1 class (to which you could apply Magical Knack to at least make up for lost Caster Level although not spell progression) and 1 level of the other.

UnArcaneElection |

Even before the SLA FAQ nerf, you probably wouldn't want two Mystic Theurges, but you could make a decent case for one Mystic Theurge + 1 Witch or Shaman, and if you didn't have enough people to get two 9-level casters and everything else you needed in the party and you knew you were going to have a lot of 15 hour adventuring days instead of 15 minute adventuring days, you could also make a pretty good case for 1 Mystic Theurge. Of course, that's all out the window with the bathwater now.