I think if you were deciding between Auto or MT, "problems" should be something that's further down the list. I think life style, fun and convenience should over ride any small problems that persist between AT vs MT and are way more important in the AT vs MT battle than anything. But as far as I know, major problems seem to persist in both. I own the MT and haven't had any issues. Check the Issues | Warranty | Recalls / TSB sub forum for more.
The two that kinda stick out are:
- RPM's dropping on automatic (until stall)
http://www.ft86club.com/forums/showthread.php?p=328355
- Rough 1st to 2nd in manuals
- Idle RPM's dropping in manual and shuddering.
http://www.ft86club.com/forums/showthread.php?t=8285