Requirements
I am developing a music game that requires access to the audio line-in and classes to help me analyze a MIDI file (playing the MIDI is NOT necessary for me). Secondly, I need a graphics engine that allows easy and quick development (within reason). The game's focus is not cutting edge graphics - think along the lines of Audiosurf.
Issue 1
Java provides easy to use and well documented Audio line-in input and MIDI file support built right into the API that I could not find with C#. I found some resources to read from the line-in and MIDI helper classes but don't have much documentation/support and seem to be workarounds to a lack of support by C#.
Issue 2
The second aspect of the game is of course the graphics engine. On the C# side, XNA seems to be the clear choice for my needs. On the Java side, I'm leaning towards JMonkeyEngine (or ogre4j as a second choice). JMonkeyEngine seems to be fine for my graphical uses but the documentation is scattered and sparse.
Deciding
Both issues are of equal importance. Also, I know the community here is prominently .NET programmers, so try to consider both languages if possible.