Mercifully I've replaced or improved many of the issues that would otherwise give me reason to list them here.
But, the following remain:
-8" front wheels (weaksauce looks/perfomance)
-Touchy throttle and notchy gearbox when cold
-Headers design/performance (so much potential here, yet BMW left us with 540 headers; alternatives cost a fortune)
-The fact that the plenum has to come off for 85% of engine repairs (makes the labor bill at the dealer go up two-fold)
-Headlamp adjusters & xenon projector quality
-No factory AUX-IN for earlier models (makes installing XM radio (properly) an expensive and labor intensive feat)
-Rear shock tower location (because removing the rear tray/deck is a PITA)
Seems like a lot, but most are trivial. When I had my E46 cabrio, however, I could write a thesis on how much I didn't
like about it.