Like many people say, there is no substitute for the Total War series. They are very unique.
Personally, as an experienced RTS player, the only RTS games I think are equal to or better than Total War games:
1) World In Conflict: similar to Total War in that there is no base building when you are in combat. However, there is no Campain map. Each match is it's own game. You also need to get people together that are willing to cooperate with you as it is a very team heavy game.
2) Sins of the Solar Empire: I like this game because it is the only good Space RTS game I have found. Game is very balanced in all regards and does not suffer from annoying problems such as the Total War pathfinding.
3) Civilization IV Beyond the Sword: not an RTS, but still very good if your looking for a history heavy game like the Total War games. IMO, no other strategy game can compete with Civ IV.
