Here's my suggestions:
So this is more of a nit-pick, but its always bugged me how whenever you use a script to add 8 directions, it would still use the other 4 moving animations. So I thought, why not kill 2 birds with 1 stone? Add diagonal movement, and change the spritesheet to support diagonal animations.
It supports this weird 6 button system (think of an older Sega Genesis controller (or an earlier one, but with twice the face buttons)) that most controllers don't use. As a result, the inputs for most controlers are very weird (X on Xbox is confirm, for example). So, I suggest that they either ditch the old controller support, and/or add better support for Xinput (Xbox) and DirectInput (PlayStation) controllers (especially if they add diagonal movement, so the basic support for the L sitck for movement will be more natural). If they did this, it could add more possibilities for more functions. And allow rumble features, if available.
This is more my opinion, but I always disliked the ingame character generator. maybe it's how the faces are staring at the screen, or maybe the front view for the faces instead of the 3/4 view of the defaults. My suggests are to not only have the view angles match, but also add more options (basically take all of the available options (both from the RTP and the character generator) and make dozens of recolors). And also add emoset support, and add behavor and damage sprites (but those last two could be a stretch).
Also some other things, like HD support (I know, it's already been said).