Amy is a main character, so I think she'll stick around next series. Maybe they'll stay broken up for a while but I hope they get engaged in the next series. And there has to be a Leonard-Penny wedding next series or I might actually cry.
I was disappointed that Howard's half-brother was only featured in one episode. That's quite a dramatic thing to happen to him and they just crammed it into half an episode and didn't make a big deal out of it.
How annoying was it that they kept stopping the series and re-starting it, though? It took about a year to get through 24 episodes!