I just finished the fic up to where it is, and have lots to say. I will start with good things:

• Made me giggle many times. I want an RSS feed and am annoyed that one doesn't seem to be available.

• I like a number of your original characters and see no glaring flaws in your interpretations of the canons.

• I applaud your choice of protagonist species and you do a nice job of making it a continuing handicap that the protagonist has to work around.

• Your pacing is good in the sense that (with exceptions to be described below) I was not typically tempted to skim past any parts because of drag or mismanaged suspense.

I will carry on with critiques, noting that none of them stopped me from reading the entire thing and wanting more:

• The musical interludes were cute once and annoying ever after. I stopped reading them. (If Missy were using them to study cartoon physics, instead of just to... occupy a couple screenfuls of text on each occasion by randomly singing sometimes... in a written medium... I would be much less annoyed, perhaps even charmed.) The chess games are even worse; perhaps that's only because I don't care about chess, but even so that limits the audience sharply for those passages.

• I'm puzzled by the way the fic handles gender identity. If I were writing about a male human who'd been turned into a female cow, even if I handwaved discomfort with being a cow, I'd write the character as trans - narration would refer to him as "he", trusted friends of said character would be asked to do the same, it would be a reasonably high priority to get sex-changed as soon as that became an available thing (perhaps on some pretense). And I also definitely wouldn't have the character go by Missy. You're handling that differently - which is one thing when it's just Missy. Star Chaser is treated the same way, with some limited interest in being changed back but with female pronouns in the narration and so on. I don't understand what you're trying to say about gender/the sex change magic/these characters/etc.

• The romance rings false throughout. I like your Cheerilee just fine, you write her as a lesbian just fine, I just don't see her and Missy being interested in each other the way you're telling me they are. To say nothing of the bizarreness of a formerly human protagonist being attracted to ponies with no further ado and being interested in conducting a relationship with one while shaped like a cow. The story purpose served (giving a personal cast to the save-the-world goal) seems like it would be handled okay if you just gave Missy one or two convincing friends, instead of pawns/antagonists/assistants/set dressing.

• You write things out of chronological order by dropping into the pluperfect ("I had taken a clever precaution earlier"; "I'd already thought of that"; "I'd given my enormous offscreen staff that task the previous week", etc.). You do this conspicuously and very often. This ruins real peril (maybe she'll just pull another pluperfect solution out of her rear), makes it harder to understand complex series of gambits (wait she did what when?), and puts a lot of emphasis on some of her less plausible memories/resources/allies that you'd do better to tuck into corners. Having her work through problems forwards is also important for the aims of a rationalist fanfic: you can follow the thought process as it goes. The pluperfect cheats at that.

• You're doing a lot of "bringing Earth science to Equestria" and also a lot of "doing the generalized scientific method to magic". They're in tension, worldbuilding-wise; be careful.

• You are juggling a lot of stuff, and you're not putting it into tidy, episodic plot arcs, either. Science! Politics! Training up the assistants in rationality! Magic! Travel! Tacked-on romance! Cameos for canon favorites! Greek deities! Other "game pieces" who you won't put out of their misery by letting them find out Missy was human too but who keep running around in the background! Jail time! Engineering! Diplomacy! Pop culture references! Collecting new friends! Extortion! Dueling! Archaeology! Spontaneous musical theater! Chess! Dependents of the lovedrunk and puppy variety! It's very busy, you're resisting wrapping up any of the plots you open, and it's dizzying. Perhaps this is an element of realism you care about; but it's in tension with the (Watsonian) realism of "there are only so many hours in a day and memories in a head for Missy to be doing all of this" and the (Doylist) realism of "I can only juggle so much content in a single story".