The overstatement of mystic theurge longevity
First of all, it’s not a given that mystic theurge has extra spell slots, even if we ignore spell levels. At 7th level, an archivist, cleric, or specialist wizard has the same base number of spell slots as a 3rd-level archivist/3rd-level specialist wizard/1st-level mystic theurge. The mystic theurge gets bonus spell slots for high ability scores twice, but the single-classed spellcasters get them for twice as many spell slots, so they even out.
And while yes, that is just 1st level as a mystic theurge, the situation doesn’t exactly improve dramatically from there. At 8th level, the mystic theurge pulls ahead, as a result of getting 3rd-level spells from each side (netting not only more base spell slots but also more bonus spells), but then at 9th they lose a lot of that advantage when the single-classed spellcaster gets 5th-level spell slots.
By 16th level, of course, the mystic theurge has 66 base spell slots, while the single-classed spellcaster has 40. So that’s nice, ish—but it’s also arguably just about the best level to be a mystic theurge. And honestly, it’s hard to go through 40 spell slots—the mystic theurge is just going to go to sleep with a ton of unused spell slots, which isn’t much of an advantage to anyone. And of course, next level, the single-classed spellcasters get 9th-level spells, while the mystic theurge gets to deal with the perennial “now what?” question.
And that’s all ignoring spell levels, which of course we should not do—a spell of level X is worth easily twice as much as a spell of level X−1.
Early-entry necessarily changes the analysis—but not really enough
All of the above is assuming 3rd/3rd entry, which is the straightforward, expected entry into mystic theurge. You can instead enter (through various shenanigans) as a 2nd/1st or (more easily) 3rd/1st. Losing one level of spellcasting rather than three on your “primary” side is definitionally a whole lot less painful.
Even then, though, the other thing that is crucial to any analysis of the mystic theurge—but missing from yours—is the assumption that having spells from two different lists is a big advantage, that there are lots of things that you get access to that way that are really worth having. After all, the cleric spell list and the sor/wiz spell list are fantastically strong, right? Well, they are, but they don’t really add terribly much to one another. Most of the best spells are on both lists. Most of the best spells that aren’t, have reasonable replacements on the other list. The things that truly are unique, and really are worth grabbing, are mostly on the sor/wiz list—intentionally, to make up for the cleric’s armor and HD and BAB—and the cleric can get the most choice options with domains. So the biggest “advantage” of the mystic theurge is basically fiction. Mystic theurge may not even be worth one lost spellcasting level.
I mean, consider: rainbow servant isn’t that popular. It’s not considered one of the most powerful prestige classes out there. And that misses zero spellcasting levels, and gets you fully-leveled cleric spellcasting. Fewer spell slots, true, but most spellcasters simply don’t care.
The one possible exception
The one possible, maybe exception where you might actually want mystic theurge is in combination with war weaver. War weaver is a 5-level prestige class from the Miniatures Handbook, and it gets the ability to store spells in an “eldritch tapestry” and release all of them at once, distributed to each of your allies (even if the original spell was single-target), as a single move action. This is phenomenally powerful. And the catch is that those spells can’t be a higher level than your war weaver level, which again caps at 5.¹ So being a 5th-level or lower spell is very valuable to a war weaver. Sanctum Spell abuse can turn 6th-level spells into 5th-level spells, but it’s hard to go beyond that. That means 7th-, 8th-, and 9th-level spell slots are not as much better for a war weaver as they are for other spellcasters. Don’t get me wrong—they’re still better. You still want them. But as consolation prizes go, compatibility with the eldritch tapestry is a very good one.
The other thing about war weaver is that it requires and progresses arcane spellcasting specifically. Its adaptation section even warns about not allowing it for divine spellcasters (thinking that tapestry-distributed healing would be too strong, which is... not really what they should have been concerned about). This kind of matters, because the cleric spell list has a lot of really strong buffs. So does the sor/wiz list, of course, which is why ordinarily you wouldn’t really want to go for mystic theurge as a wizard just to get them. But when you can prepare a whole suite of buffs that you can release as a move action, you want everything you can get. And maybe the extra lower-level spell slots is worth something to you, so you don’t have to worry about whether or not you want the whole suite for every fight—you’ll have the slots, so of course you will.
But then when you consider other ways you could use high-level spell slots as a war weaver—say, metamagic—and you start thinking that those ten levels could be better spent as, say, incantatrix. Which, OK, it’s incantatrix, so of course it’s better, but it’s important to keep in mind the competition. If nothing else, once again, rainbow servant... looks to be a fair bit better, even if you “could” use the spell slots.
If you want to control a lot of undead minions, divine spellcasting can have rebuke undead, and also gets desecrate. These are great advantages.
On the arcane side, minion-mastery is less of a focus of necromancy—it’s more about curses and, strangely enough, buffs. The one notable arcane-only spell for an undead minion is animate dread warrior, a 6th-level sor/wiz necromancy from Unapproachable East.
So a mystic theurge could, in theory, have both of these. Except their rebuke undead is truly anemic, because mystic theurge doesn’t advance it, and they’re substantially delayed in getting both desecrate and animate dread warrior. The true necromancer prestige class does exist, and that advances rebuke undead, but then it also misses on more spellcasting levels. Either a cleric or a wizard would be far better off trying to just poach the one spell they want through some other method, and in the wizard’s case, trying to get rebuke undead somehow.
Or, easier, one could just be a dread necromancer, which gets rebuke undead natively on an arcane spellcasting class, gets the best benefit of desecrate as a permanent class feature at 8th level, and can easily learn animate dread warrior through its advanced learning feature. If they make the effort to also learn desecrate—which takes a little more hoop-jumping but is certainly possible and stacks with undead mastery—then they’ll easily be the strongest leader of an undead army available. This is vastly superior to any mystic theurge or (shudder) true necromancer build.
- Barring legacy champion abuse.