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.
The plenum thing is definitely annoying. It doesn't cost me anything since I DIY everything, but it is a pain. I just did it AGAIN yesterday as part of my latest round of repairs. I actually timed myself yesterday - 25 minutes to remove it at my normal pace. I'm sure some can get it off quicker, but I think the first time took me well over an hour. At least all my little hoses (oil separators, etc.) come off easily now since they get removed regularly! I break the 4200 bolts loose with a hand ratchet, but pin them out with my electric driver...letting them fall where they may. I then snag them each with the magnetic pickup tool. Double all times when you drop one into the abyss of the engine compartment!
People complain about the weight...its a big 4 door sedan with a really nice motor to compensate for it. Its not an M3, its not a Z4M, its an M5...its gonna be a little heavy. And I can take turns as fast as I want to. Its either going to stick, or break loose into a controlled and completely exhilarating drift. The weight makes it fun.
I just rode in a 1,700lb VW Golf that just had $50,000 put into it including a huge turbo and various other engine mods. Not impressed. Didn't throw me back in the seat like the beast.
As for the price of the upkeep...for all the money spent, the car sure gives back! I always laugh at how I many times I tell myself "man, I love this car".
I'm an electrician and I own an M5!! Mine just isn't parked in front of a million dollar home or in the garage next to my other car, a Porsche GT3 RS. Depending on how you look at it that tells me the car is pretty affordable.