Metal Fatigue is a pretty good overlooked RTS
It's main gameplay is focused on constructing mechs using component pieces. instead of building Mech A, you build Mech Arm A, Mech Arm B, Mech Torso A and Mech Legs C, or any combination thereof, and then put them together. Enemy mechs will occasionally drop their components, which you can then reverse engineer and construct for yourself, allowing you to get the different weapons and abilities of your enemies.
The resource system is based on building solar panels on an "orbital" plane above the battlefield where asteroids are located. You "building" units can fly up there and build satalites. These asteroids and this orbital plane is in full view of everyone however, so if you build solar panels right above your base, the enemy will see that, allowing them to pinpoint your location. Later versions of mechs can fly upto the orbital plane and destroy the enemy's solar panels, or protect their own from similar destruction.
There is also a cave plane below the battlefield, where only the inferior tank units can traverse. There may also be resource gathering in the cave plane, but I can't recall exactly. Tanks are good against buildings, but weak against enemy mechs, so you can use tanks as a sort of flank.. Burrowing underneath the enemy's base, distract the enemy's units with your mechs, then raise your tanks up in the middle of their base and destroy their buildings.
There are 3 factions, one of them gets upgrades to the melee mech pieces, one of them gets upgrades to the ranged mech pieces, and the other gets special mech torso pieces with weaker weapons, specialties like cloaking and detection abilities.
I remember having a huge amount of fun with it, but it's a game you never hear about
It's Metal Fatigue, if you didn't catch it in the first line.
edit: Also, if you like turn based strategy, Alpha Centauri is basically Civ 3 on crack, and in space.
Entire books could be written about Alpha Centauri and it still wouldn't be enough to convey the awesomeness of it. It's far deeper then any other Strategy Game that I've ever played, including Civ 5.
