The button lag, ugh.
Well, actually that was only a problem for me when I first started playing online, I noticed it on my very first online match. I got used to it after a very short time though.
Here's hoping Smash 4's online will play smoother, less lag (or no lag. A Smasher can dream...) and will have more options. (perhaps have an online Smash chat mode? That way you can find friends more easily and communicate with them more easily as well. If Bosses return, they should allow boss mode to be playable with friends online as well)