I went to E for all so I'll contribute from my experience with him.
As everyone already knows, he's definitely the fastest on the ground, not in the air. I was stuck in melee mindset and kept thinking SHFFLing was the best way to approach so I spent too much time in the air and actually didn't need to deal with his ground speed that much. That said, his ground speed actually makes landing his running moves, runningA and running grab, easier instead of harder since Sonic covers a lot of ground during them, provided you don't run past your opponent first =D (his running attack is spinning along the ground and it covers a lot of distance, maybe 1/3 of battlefield).
His neutral B and Side B probably contribute to the OMG I can't hit anything factor. The homing attack has does a poor job of homing in on anything that's actually moving. The instant (or random?) hopping in his side B also seems a bit weird, but I'm sure that within a few hours, someone will figure out its mechanics, and it won't be a problem anymore. On the otherhand, his DownB is significantly easier to control than Jigglypuff's, since Sonic can actually cancel his with some attacks.
I had a lot of trouble Dash-Dancing but I attribute that to the classic controller. I fear for anyone trying to dash-dance with a wiimote ...
The only "clunky" experience I had was with the smash balls. Sonic's so puny it takes forever for him to open the darn things.
As for non-control issues I did experience a bit of problem finishing people off. Sonic is also incredibly weak, with few moves doing over 10%. I think this will actually be the strongest discouraging factor, since you really will probably have to hit your opponent twice as much as he hits you. Granted with his incredible speed and assuming that gives him good comboes as my experience in the Demo seemed to indicate, its probably not an issue in the hands of a good player, but it could definitely discourage someone who hasn't yet mastered his speed or any comboes.
In conclusion, I don't think Sonic's difficulty in control will be a serious barrier to anyone with a bit of dedication, but it might stop some beginners from automatically picking him up as their mains.