File Format Specification
While MuseScore uses a xml-bases file format it can still be considered to be a proprietary file format, due to the fact that there is absolutely no specification about how this file format works. And this is bad. This means that anyone who wants to interact with MuseScore will have to reverse engineer the functionality, and it might change anytime.
This means that developing tools for MuseScore files is very hard to do. For example, someone might want to convert a musescore file to another format, or extract specific information. Or in the other direction, a program might want to pass music to musescore for engraving. One could have a LaTeX or OpenOffice Plugin for inserting scores into documents.
So I think MuseScore should start to keep an official specification of it’s file format.