To change the charset, edit section 000 of Metadata.txt.
I tried changing the charset, by copying the current charset Red.png and pasting in some other images (another charset with a blue background), but the problem is that the background is no longer cut out ingame. That is, there's a large white rectangle around my character. How does one get rid of this?
Also, this may be inconvenient for a lot of people, but is there any chance the tilesets can be rearranged/split to make them a bit more manageable? You know, floors, foliage, rocks, fences, ledges, buildings all in one spot? That'd make things a bit easier to work with, since you'd know all relevant (i.e. relevant to what you wanted at the time, e.g. a tree) tiles were in one place. They're mostly together already (I'm talking about the OverWorld one here, but it could apply to Inner as well), but there are still a few random trees and grass around the place. Not to mention the PokéCentre and PokéMart tilesets are missing a few textures (ones I've noticed: Computer monitor (Centre), some shadow floor tiles(Mart)) - they all seem to be in the Inner tileset, so they're just a case of copy and paste. A few tiles also run into others (e.g. bottom left of the round brown table in Inner, near the first bed you come across).
I'd offer to do this myself, but my spare time is sketchy at best (final year of University and all). Sorry.
Finally, I've noticed that when using a Rare Candy, there's a little text bar at the bottom asking which pokémon you want to feed it to. That's fine, that's how it should be. When you use it, another text window appears saying the pokémon levelled up, but then that text window disappears when it then shows the stat increase/new values window(s). This leaves the little text at the bottom asking which pokémon you want to use it on, while you're busy looking at the results of you having already used it, which looks wrong. Any chance you can get that text bar to stay throughout the stats?
Otherwise, a great piece of kit. Too much praise is not enough.