There's only 2 things about the second season I didn't like.
1. The incest factor, was a little weird, but oh well.
and
2. Him saving Asuna, the whole "rescue the princess" plot. It made for some cooling ending sequences (both in Alfiem and in real life) for Kirito, but it kind of ruined Asuna's character. The point was that she was this bad ass chick that could also kick ass, and then they made her a hostage.
I still love SAO as a whole though, Asuna x Kirito is so Kawaii, and I found the action was pretty awesome. It did Shonen well IMO, but eh.