A lot of Elite 4 in previous gen's have had a lot of opportunities wasted. Not much is known is about Will, Karen, Bruno, the entire Hoenn 4, etc. and I think that is a bit of a waste.
Also I would have liked it if the PC from BW was in BW2, the story had set it up perfectly, but it was only a tease. It could have been set up like N's initial battle with his Dragon, except with the opposing Dragon and Memory Link could have been used to designate gender and name. It would be cool to see that the region in hypothetical gen 6 is where N and the PC went. It's very unlikely, though.
Also I want N to return because he makes me have weird feelings in my heart that I'm not brave enough to face yet.