Horde: We have leaders left to kill? I guess Galywix because he isn't very interesting, and he is annoying for the 3 seconds you see him. Sylvanas is getting a bit old-hat by now, but she is still interesting enough to keep around. Baine also needs Sylvanas as a counter point if he were ever to actually do something. Lor'themar could get a good killing too.
Alliance: It would be really interesting if Anduin was killed. It would create a power vacuum and actually give the Alliance an "in-fight" because they don't have that. Personally, get rid of Malfurion and Tyrande. They are written awfully and anytime I have to interact with them I can't wait for them to be away from me. I don't hate Genn so much, there is more to do with him. He'd be incredibly interesting to see if they did kill Anduin, the difference between him and Velen would be great.