OK, I have now read this whole thing. A couple of things struck me:
The three listed annoyances -- money, weight, cleanliness -- seem to share the common theme of a lack of discipline. That in and of itself could be good, bad, or neutral; that combination of personality traits can mean "life of the party" or "fat slob" or "clinically depressed" or anything in-between. The real question is how does that mesh with OP's personality and desires? OP seems very ordered and disciplined; finances under control, high level of cleanliness, etc. So is the GF appealing because OP feels a little too would up and likes her softer edge because it balances him out a bit? Or does he love her despite that and will only be happy if she can shape up a bit? From what has been said so far, it sounds like the latter -- in which case that is the issue to focus on. He needs to figure out whether she is actually interested in and able to modify her behavior to meet his minimum expectations, or whether he can modify those expectations and accept her for who she is right now.
And towards that end, where do these traits come from? E.g., maybe she never had a good role model, and her parents told her that a college education was the ticket out, no matter the cost, and OP is the first person she has been close to who could show her what good money habits involve -- in that case, is she willing to learn, and is she interested in making a serious, lifelong change? Or does she not care that much -- or does she not have the ability to sustain the effort -- maybe she jumps in with both feet but then backslides when it gets hard? Does she try to eat reasonably well and get some exercise, or is she sitting on the sofa eating bon-bons? Or did she used to be more disciplined/better at managing all those things, but then over time got overwhelmed with the money and the efforts to maintain her weight and just spiraled and shut down? Has she been screened for depression/anxiety? Etc. etc. etc. Some of these options would make her and OP a good fit, and some of them will just result in more and more frustration as the years go on.
IOW, to me it is all about context: not just what she does, but why -- and how that meshes with what OP expects from a partner. We have all done completely dumb-ass things in our lives -- sometimes even at ages by which we damn well should have known better. OTOH, many of us have also tried to change and not been able to keep it up, or felt like we needed to pretend to be someone we're not to make someone else happy. Both OP and the GF can be completely reasonable people with completely reasonable approaches to life and still not be the right fit for each other. And on the flip side, the GF could have been a a completely immature, irresponsible looney-tunes during her 20s and still be a good partner for OP now. We can't possibly know which one it is with the little information we have.