Hey, I've actually had plans on trying to make a Cave Story RPG myself. I even tried making a webcomic (which I never uploaded) about the plot. Like, Quote in the weapon shop of Mimiga Village: "You sell
wooden guns?" Shopkeeper: "This is the first town! What did you expect? Iron?".
I was going to have a style of sprites like this:
(Characters are custom FF1 sprites from TSR). I'd have made custom sprites in that style (Fire Emblem, I think), and had a gameplay more like the SNES FF games, but with focus on battles that looked more cool and fluent (like Chrono Trigger's system).
Also, I'd planned some more unorthodox stuff, like having the Hermit Gunsmith being the first new party member. And the whole game was aimed at being more funny that serious.
Luckily I never got started. But I think I might have Quote's battle sprite lying around somewhere. Want me to search for it?
EDIT:
Read about your trouble. Feel free to ask me for advice, I have some years of experience with Game Maker (though I've never done and RPG, my most advanced game is Gun Princess (in my sig), a game trying to be better than Cave Story). And I'm writing a book called Guide To Cave Design as well. While I focus on Metroidvanias, I know quite a lot about game design in general, and I'm rather creative. So, as said before: if you need advice,
call me. I'm at the GMC as well, and my username there is Yal as well.