As far as rushes go, I think the real solution to them is simply to incorperate it into the game.
That`s the problem - we are talking about MMORTS here. So in most cases player would attack a fully-blown base. So conventional rushing with lethal result just won`t work. However, we did decide to include some 'original' ways player can rush another instead - after all what is rushing? Just an attack very early in the game, using very limited resources, fighting against time, and a lot of micromanagement.