The A380 is probably the smoothest flying plane I've been in, but in my experience it has one slightly annoying behavior quirk that degrades from my ability to enjoy it. Granted, I've only flown in one a few times, so I may have just been unlucky. But at cruise, the autopilot surges and coasts on a slow repeating schedule. Ease off and float for a bit, get just a little bit low and throttle up slightly to catch it, rinse and repeat. Not terribly noticeable when awake, but when I try to sleep I'm acutely aware of that sensation.

So far my personal favorite is the 787. About the only thing 'bad' I can say about it is that all the mechanical bits are kinda loud, like the flaps and stuff, and are very noisy inside the cabin. But it cruises so nice, and the lower pressurization altitude and increase in humidity is noticeable on a long flight.