Great work on the guide, and very timely, since I've just started playing a Mystic Theurge in Rise of the Runelords. He's a cleric of Nethys so the whole "all magic is power" thing fits very nicely.
Just a couple of comments.
For advancing past Mystic Theurge, Exalted is excellent, given that (unlike evangelist) it doesn't lose another casting level. I don't think you can use it to advance MT past level 10 - after all, it's a 10 level class: what's to advance? You could, of course, use it on your original class. But one other trick you might like to consider is using it (or similar prestige classes) to advance MT itself. The level 10 MT capstone is very, very nice, but the only other thing you get (Combined spell) is kind of underwhelming. There are times when it will be very useful, but most of the time, you're likely to just use your spells as-is. Using - say - Exalted to advance MT gives you several great class powers, a better BAB and hit dice ... and RAW still advances your dual casting progression.
The other thing is that your guide is very focused on being the ultimate caster, which means getting casting on both arcane and divine sides as high as possible. But another option is to use MT as an augment to one class. By using the SLA method of entry, you essentially qualify for the cost of 1 level. Sure, you'll never excel in your second class, if you focus on the primary one, but it opens up a bunch of options.
My current build is a combat MT with Magus/Cleric. The focus is on Magus, so the build stub is Magus 7/ Cleric 1/MT4/Exalted5 (the GM has already informed us that we will be finishing the adventure path at lvl 17). This build includes most of the good things about Magus - armoured casting, spell strike, arcana - but also shores up some weaknesses (limited number of spells, low HP for a front liner) with 6th level spells on both divine and arcane sides. Not as powerful as a full caster agreed, but just as viable - and more fun, I think - than a straight magus. The additional number of spells more than makes up for the loss of things like greater spell recall, and the cleric list contains many great buffs (or rebuffs) that help in combat.