I was giving this some thought and here's a feature I REALLY hope to see, and one that would put the VTT well ahead of others.
1. The ability to designate tokens as allies.
2. The abilty to have aura (and aura type abilities like a warlord's initiative bonus) take automatic effect on allied tokens.
That would be great. I know that when I've used Maptools, I've forgotten leader auras from time to time and, when playing a warlord, I constantly have to remind the others to add their initiative bonus. Having that sort of thing built right in would be fantastic.