It's very difficult to answer. I forgot to mention I also played Disciples II with all DLC, but never finished with elves. Battle for Wesnoth is one of the games from previous century, to which I return. Total War: Rome II was also good game. But my most favourite are probably these two: Conquest of Champions, Supreme Commander: Forged Alliance

The first one - Conquest of Champions, or as renamed before closing the server, Heroes of Galandria is gone and never to return. It was a card game, where cards became living soldiers on a battlefield. It was only for hardcore strategists and had troubles finding new players and convincing the old ones to pay and is now gone forever (though devs said 3 years ago or more, they will return one day).

Supreme Commander is one of a few games I encountered, which uses AI to choose various strategies. If you opt for random, it might become Adaptive, Rush, Turtling, Land, Navy, Airforce or Balanced kind. All AIs are difficult not only because of simultaneous orders (you can do too when you stop the game), but are also well-programmed. The game itself is a strategy at its root meaning. You can have hundreds of tech-1 interceptors. Two dozens of AA gunships (tech-3) or superiour air fighters (tech-3) or a battleship can take care of them.
The development of technologies is very interesting. You need to build a factory (land, navy or air). Upgrade it and build an engineer to proceed to the next tech. Only this engineer will be capable of building tech-2 buildings except factories, which always start at tech-1. On tech-3, there are also experimental factories, which build an all-powerful units, but it takes them about 10 minutes. Tech-3 units in general build about 2 minutes, while tech-1 can be build as fast as in 6 seconds.

Both of the games met the same destiny. They got dumbed down. The first one is dead not only because of it. The other was followed by Supreme Commander 2 and gave up all its unique mechanics for a boring skill tree. Then, the Gas Powered Games developed Planetary Annihilation, which has new mechanics and is a bit similar, but very difficult to play. As owning multiple planets and having to turn them all around to find your base or that of enemy is just not the right design choice for RTS.

I wait and I hope for an RTS strategy like Total War series or Supreme Commander, but with self-learning artifical intelligence. It is already possible to develop it. There is a bot, which masters DotA 2, the bot, which has ELO of about 1600 in Chess I think (world champions have only about 500 more). Such game would bring life back to RTS genre.