Hi, thanks for using our app!
Yep, about the MIDI music you are right. We are using different instruments (so called patches) as the original soundfont shipped by Windows (which RPG_RT.exe uses) is copyrighted.
Currently it is not possible to change the MIDI soundfont or patches without recompiling the app.
However, you can of course convert the music files beforehand, you just need to keep the filename.
battle.mp3, we support MP3, OGG Vorbis and WAVE music.
About the battle issues: Well, our interpreter is not complete yet and the battle system has a lot of unimplemented stuff, however we have lately improved it quite a bit.
We track our issues at GitHub, you can add additional issues there. However, we already have a lot of battle related issues (https://github.com/EasyRPG/Player/labels/Battle), so yours might be already present.