[Variant] Never Behind the Curve

[I_Got_This_Name]

Working on some of the things you mentioned.

I don't think any other classes get Paladin Mantles (I've only seen them in paladin fixes), so I don't think that's an issue with Divine Mission.

Magical Study is probably the most powerful of the options here, and, yes, a Wiz5/Sor5/Clr5 can cast 7th level spells as a Sorcerer, and 8th level spells as both a Wizard and Cleric (but only two spells of each level from each of the latter classes, plus domains and bonus spells, of all levels above 3). They've traded their ability to fill in their casting behind their highest level for casting of two other classes. A Wiz5/Clr5 with Magical Study in both of them is flat-out better than a Mystic Theurge, because the Theurge sucks; this keeps them able to cast their highest-level spells.

Let's take a 5/6 (or 5/5/1 in something else) Wiz/Clr example, and compare to a 3/3/5 Theurge. The Theurge casts as an 8th level in both classes, casting 4th-level spells. This casts as a 5 or 6, but with two slots available at 4th and 5th level, and one sixth-level slot each. This character can contribute to a party containing a pure wizard or cleric without necessarily overshadowing the pure caster; they have more 6th-level spell slots base (one for wizard, one for cleric, one domain, maybe one for specializing, vs one for wizard and maybe one for specializing, or one cleric and one domain), so anywhere from 1.5 to 4 times as many, but fewer lower-level spell slots, and, more importantly, fewer bonus spells. It's much easier to get 22 int at 11th level than 22 int and 22 wis. Further, this character still has the same number of actions.

The Theurge cannot contribute. Assuming wisdom and intelligence both between 18 and 25, with items, and a specialization, the Theurge has eight 4th-level spell slots (two Wizard, one int, one specialty, two Cleric, one wisdom, one domain), and nothing higher. In four encounters per day, it can cast two 4th-level spells in every fight. The other caster, admittedly, has three fewer 4th level slots (three normal, one bonus, one specialization or domain). They can then do exponentially more with their four fifth-level slots (two normal, one bonus, one specialization or domain), and three sixth-levels (one normal, one bonus, one spec/dom). If they chose to prepare all 4th-level spells, that's twelve slots, to the Theurge's eight. Since the power of spell levels grows at a rate pretty close to exponential, that's a fairly stupid idea; more likely, they'll be casting one or two spells of 5th or 6th level per encounter, with the occasional lower-level spell used for combos or to look like they're doing something. The primary caster doesn't even cast the kind of spell that the Theurge has as it's best spells, because they're not significant.

The pure wizard or cleric has exponentially more power than one who has lost caster levels; the only way to make up for it is to not charge them caster levels. Nobody who wants a reasonably powerful caster character loses caster levels, even though some pretty interesting concepts can only be implemented by doing so. Mages, more than anyone else, need this to keep up (among themselves. Nobody is ever saying that primary casters need anything, other than perhaps a very severe nerf, to keep up with fighters).

Admittedly, yes, I picked a level where the Mystic Theurge is down two spell levels instead of one. At, say, level 10, the Theurge has six 4th-level spells, while the primary caster is no different, except missing the 6th-levels (5/4, for a total of nine slots, four of which are exponentially better than the Theurge's). The Theurge cannot teleport, nor dominate; it casts 1.5 fourth-level spells per encounter. The real mage, burning at the same rate, casts 1.25 spells of the same level and one fifth-level per encounter. The big selling point of the Theurge is that it has twice the casting ability of a normal character (three levels lower), which gives it even more endurance, and it doesn't even have that, at least with spells big enough to be worth combat actions. Unless you're badly hurting for someone to hold the healing wand, you could replace the Theurge with a wizard, and come out better 100% of the time. Few battles/day? Then those higher-level spells mean that you can do more with your actions, which is good since you don't have so many. Long day adventuring with lots of fighting? Well, it's a good thing you have 1.5x as many useful spells as the Theurge does.

If you wanted to get really mean, you make the main caster a Sorcerer, and give him a Cleric cohort. That has even more power output, since it has two actions per round, and still has more, higher-level spells than the Theurge.

"Hi, Mystic Theurge of my level. I'm Batman. Have you met Robin? He outperforms you on a round-per-round basis, and the two of us outperform you on any other basis. Yes, this is a perfectly fair comparison; I spent a feat on him."

Now, for the Magical Study comparison at 10th and 11th level. We'll only compare slots at 4th level and higher, since the lower level slots don't really matter. The multicaster has fewer low-level spells, though.
Normal caster: 5/4 at 10th, 5/4/3 at 11th
Magical Study gives two 4th level and two fifth level class slots at 10th character level. With bonus spells and specialization, that's 4. Times two for two classes, that's 8/8, 16 spells, as opposed to 9. Raise to 11th, and it comes to 8/8/6, 22 instead of 12 (14 instead of 7, counting only the top two levels). Admittedly, that's a lot of spells. We don't care that this caster was weaker at 9th level, since the campaign could easily be starting at 10th; this caster can, likewise, handle its MAD. Still, most combats won't last long enough for this caster to be significantly different from a normal caster, except in variety; they might cast, at 11th level, a 6th level Wizard and Cleric spell in a combat (they can afford to cast 3.5 of their top two levels, or 5.5 of their top three, though, but the battle might not be long enough), instead of a 5th level and 6th level Wizard spell.

Admittedly, I can say that it is a little overpowered (by comparison to other classes in its tier). I could drop bonus spells from it, and/or maybe the specialization benefit and domain spells, maybe?

Superior Study is supposed to be powerful. It, essentially, allows a 5th-level wizard/5th level something else to miss nothing in casting compared to a 10th-level wizard. The downside is, though, that their other features are still those of a 5th-level character, and so might as well not be there (they might have, say, the hit points of a fighter multiclass. Either wizard, meanwhile, can spend a few cheap spells and not get hit) until 15th level, at least. Yes, Superior Study adds "Spellcasting: +1 level of existing X" where X is the class you pick Superior Study for to every level of all other classes. The Neotheurge here is a Wiz5/Clr5/PrCs10 with Magical Study and Superior Study in both classes. I should probably trim a little off of it, but I don't want to take too much.

Skillful is designed for the sneaky rogue who wants to multiclass, say, fighter, and not lose sneakiness. There are options that are more attractive in combat, certainly, but I like Skillful myself and would definitely at least consider it.

The Monk's Ways were really just groupings of Monk class features that, in between them, cover most (but not all) of the Monk, designed into the "offensive" and "defensive" path, although Fist includes some defenses. They let a monk keep up, while still holding out on the "juicy" class features (ooh! Timeless Body, Empty Body, Quivering Palm!)

Edited to add: I'm considering making Way of the Soul not be the only thing that improves your saves here; specifically, I'm considering adding saves to Combat Fortitude (the new ability split from Combat Aptitude), and possibly a few others (if Magical Study didn't need a nerf, I'd consider it); possibly only have these affect specific saves. The wording I'm considering for CF, in that case, would be something like "in addition, if you have at least five levels in classes that have Fortitude as a good save, your base fortitude save is always at least 2 + 1/2 your character level." I don't think saving throws are worth their own ability here, although they could be (that ability would be objectively weaker than Way of the Soul, but not cost 5 monk levels). If they only affect specific saves, Reflex saves would go to either Ambusher or Skillful (if Skillful needs to be buffed over Ambusher, that's where it goes).