Well, for me, the tacky use of folder navigation is a big one. I don't like the way the X3 manages music. It is quite contradictory to how I have my music setup on my computer. The other issue I have is the various problems with different audio formats. Most of my music is FLAC, but I have some WAV, ALAC, AIFF, etc. that I don't want to convert just because the X3 has problems for example with AIFF. Overall I think most of my issues are with the UI. Which typically can be changed and updated via firmware so that is good news. But it seems like a lot of the issues people are having are already said not to be resolved. If you follow the X3 thread, some of the people that already have it - have issues - ask James if they will corrected - and he says no, this is not possible. What? How can simple issues such as navigation not be fixed/changed via FW updates? I don't know, it seems like a lot of trouble for something I would only be using on-the-go (i.e gym, school, etc.)
Obviously this is IMO, YMMV.