In case you're looking for something that may fit your criteria...
Warzone 2100 is an amazing game. It's what gets me to replay the game every so often. An RTS, though I think RTT (Real Time Tactics) would be more accurate here. Choice of units matters (for ex: a main force of anti tank and anti infantry units, an auxiliary force of artillery units, another force of air support... Using these tactically is the key to victory). A special commander unit exists that increases your forces effectiveness and determines the course or movement/attack. When managed right, units obtain ranks, increasing their effectiveness and survivability. These units can be recycled to reclaim their ranks and generate better units with those ranks. You can slow down the game (and practically pause it), speed it up as well.
There's two types of missions in it: the main map, which expands multiple times. As you progress through the missions, the map expands, you unlock new technology (buildings, units, etc), you get to use the base to defend against enemy attacks multiple times.
The other type of mission consists of using your base to send out units to surrounding zones (to reclaim technology, for ex). These surrounding zones are separate maps connected to the base on the main map.
There are 3 campaigns in it. I highly recommend Warzone2100. Oh, and it's open source these days, and available on multiple platforms.
I've already seen Mindustry mentioned, but also an amazing game. It is less RTS and more resource management / tower defense. Also free and available on multiple platforms.
Shepard.