(Yes, I'm reading old threads.)
The AoE vs WC3 debatte is a bit pointless, because they were both decent games. My personal favourite are the Kohan games (Kohan 2 - Kings of War being the newest), but unfortunately they were all sleepers. Still, I think they're much better RTS games than AoE and WC. Of course, it's all a matter of opinion. And to stay on-topic, Glest is clearly the best RTS in the open source genre.