Lack of dipsticks/measurement views on bottles, etc; the door creak, the shitty "voice dial" function that doesn't understand something as simple as "Dial Jennifer," the fact that I cant disable the satellite radio that I dont want as an option when trying to cycle through stereo features on the wheel, the lack of a spare wheel, the run-flats (that will not be replaced when I finally wear them out), the "womp womp womp" that happens when you have the sunroof at the full open (wagon so bigger sunroof) when going above 20mph, the automatic wipers that think a light mist is hurricane sandy and take 10 minutes to turn on the lights. And, most of all, the brakes that produce more dust than they do braking power (will be replaced with EBC soon enough).
Im sure there are more things. Dont get me wrong, best car Ive owned so far, just not perfect.
Edit: Oh and seat belt bong. I will be disabling that. I wear it religiously but I dont think I need to put it back on when going 5mph in a lot.