Sorry it took me so long to reply, been busy.
Anyway, as far as paragraphs go, that's more of a grammatical lesson and less to do with constructing theories. All I can advise on that is to separate main ideas into their own paragraphs. If you think a paragraph is getting too bulky, try breaking it up at a point where a pause/transition would work well.
Generally I try to approach writing a theory as if I am completely clueless on the matter. Like, I may have been thinking about a theory a lot, but that doesn't mean it will be easy to follow for other people. So, almost mechanically, I try to write out, step by step, how I approached my conclusion. You may want to write your theory at the beginning of the topic in sort of a thesis statement (eg "I think Xehanort is blah blah") and then show how you deduced/induced this. This is especially true for longer or more convoluted theories where you may lose the reader's focus and they may begin to wonder why you're saying this or talking about that. Always tie everything back into your main point(s).
There are almost always gaps that you need to fill out and which might appear to be a bit of a stretch. If this is the case, let your reader know the plausibility/probability of what you're saying just so it doesn't come across as a fan fiction. Additionally, you normally ought to provide quotes that are relevant to what you're saying. If Nomura or some in-game dialogue backs up what you're saying (or at least can be interpreted that way), you should definitely include it.