Some place to set my phone. Better door pockets rather than a net. Manual key start (at least make it an option). Dashboard that made more sense (like rotary tach display). Speed latches rather than bolts to remove the top (like they have on the front panels). The already mentioned cup holders...
I hated the stock steel wheels when I saw them. Found some 17" BadLands take-offs locally and put a more aggressive stock size tire on it. Much happier with the look even without a lift (that would look pretty funny). I did see a local owner that painted his steelies black. Improved it a lot...
only regret is that I didn't get the modular bumper. Build quality is excellent on mine. The panel gaps are all small and consistent, paint flawless, everything functions correctly (so far)...now if I can just get used to not slamming the doors!