Oh, if we're including mods, the mod "Litcube's universe" for X3 is the single best implimentation of an RTS I've ever seen (And it's built into a space sim). It would take ages to explain all the functionality, but you build your own fleet (and infrastructure/supply lines) and fight against 2 enemies that constantly (and sometimes exponentially) grow in power.
1 is a fully programmed from scratch bot-style faction that does everything the player does, within the same rule set (So you're competing with them as soon as you start the game). The other is a gradual alien threat that slowly expands across the galaxy with extremely powerful forces.
It has high level orders you can give, so for example, in my current order (I'm extremely late game), if I'm attacked my ships will jump into the sector to defend me. My missile ships will launch swarm missiles at fighters, and engage at max distance. My carrier (Only 1 so far) will launch it's ships, the light fighters will protect my missile ships/capital ships, the heavy fighters will act as a screen, engaging enemies that go for the carrier, and my scouts will harass their missile ships. There's another 90~ rules I have set on my army, but that's just an example.
You also need to grow the market. Seriously. The universe starts out with a pretty big set of demands (goods per hour consumed vs produced). But, if you take missions to set up stations for the NPC factions, you actually end up growing this demand naturally, which shapes what you decide to build for your own production.
The only issue is the game's designed to be played in the hundreds of hours :P
Check out Skyrim's "PsiKotics Necromancy Mod" as well. That combined with OBIS (organized bandits in skyrim, high difficulty settings), Paradise halls (Slavery), scarcity (Less loot/gold), skyrim unleashed (Removes level scaling), achieve that! (Gives some rewards for new achievements it adds), Dragon soul to perk point conversion (Lets you convert dragon souls to hp/mana/carry weight/perk points), EFF (Extended follower framework. You can teach your followers spells etc), civil war overhaul (A+ mod) has basically turned it into an RTS for me, because the only way to deal with the difficulty is to maintain an army of undead/slaves. It's actually been a really unique and fun experience so far (8~ hours in). My current army is 3 undead thralls, 12~ zombies, 4 hirelings/mercenaries, a ton of ghosts/draugr. Fighting a civil war battle (They can be lost in civil war overhaul as well) basically means throwing my 50~ unit strong army against a ton of guards/mages, and trying to find the stronger warriors to ressurect in the middle of the battle.
