Thanks for letting me know about the current transcoding capabilities. Like you mentioned you can make some fairly accurate assumptions, or actual queries, for ipods and MTP devices, but USB devices could theoretically accept anything.
Also concerning activesync, I'm not sure if you have looked into this yet or not, but both WMP and winamp activesync device support forces files to be placed in <Artist>\<Album>\ directories with no possibility of customization, and that is artist, not album artist. When deleting files from a device, at least winamp does not delete empty directories - leaving quite a mess on devices especially when multi-artist sountrack albums are synced.
Other syncing ideas (which you might already have implemented) is options on artwork handling, such that when syncing files it automatically handles artwork based on the user's choice. For example your computer libarary might have artwork for each album stored as a .jpg in the album folder, but for the portable device you would like the artwork embedded in the file (if the format supports it). Another idea is that in syncing playlists, that MusicBee also creates a playlist on the device that can used to play back the songs from the device. I haven't found many music players that can successfully transfer a playlist and the respective files to a device and create a playlist on the device correctly referencing the files on the device for playback from a program on the device (in this case I'm speaking of the Windows Mobile platform).