I'm not a composer, but I do know a few things about music and how it works in fan games.
Firstly, keep the music consistent in regards to sound fronts. It looks horrible to have a GBA soundtrack clashing with a Gen 6 one.
Secondly, make sure the music is relevant to the area where it is playing. I can't stand music that doesn't suit an area well.
Thirdly, avoid having silence in a map. There are some instances where it is good - as in important moments, but try to have music playing to engage the player. Roxie's Gym in Black and White 2 had such a great theme, but the music vanished as soon as you beat her!
Those are just a couple of things. I'm sure there's so much more too, though.