The alert system is nice but the show new replies I think people will like better. It is one of those things that you have to use to appreciate. I have seen some people mention that they would like to see it on vB. The response they get is to subscribe to the thread. It's not the same.
It would be nice to have a link that shows replies to your threads that does not go away until you go into the thread. Well at least I would think it would be nice.