As a disclaimer before I start, I don't play many RTS games. I played Star Wars: Empire at War extensively, but only against the AI. I've played Heroes of Might and Magic III. I've tried Warhammer 40,000: Dawn of War, Starcraft, Achron, and a few Command and Conquer games. That's pretty much it. So this article won't be extremely long or in-depth.
But there's a reason for that. I like games with good stories, and as a genre, RTS games are terrible at telling stories.
RTS games are meant to simulate large-scale war with more units on the field and a wider tactical view than most games. You gather resources, construct defences, and build your offence to take down the enemy in large battles featuring potentially dozens or hundreds of units on each side. And in games that offer multi-battle, back-and-forth campaigns, the focus is even larger.
Think of it in terms of a real-life war. How easy is it to sum up the story of, say, World War II in a concise yet accurate way? We want our stories to be personal and relatable, but something like a global or galactic war is far too big to include an emotional and personal narrative as well as a full understanding of the scope and scale.
One of the main difficulties with an RTS game, in terms of the story, is defining the narrative role of the player. You're a supreme omniscient commander running an entire war - how do you personalize that? The RTS games I've seen tell their stories primarily through cutscenes and not during actual gameplay, so even if the commander is a character and there's a strong narrative, the story and the gameplay are kept fairly separate from each other and don't interact much, aside from some voiceovers during missions. In that kind of set-up you don't really need to play the game to experience the story, you could just watch it on YouTube.
I'm actually not sure that there's a good way to integrate a strong, personal story into the gameplay of such a large-scale genre. I'm at a bit of a loss, and I may just have to conclude that RTS games aren't really for me. If you have any ideas, though, I'd love to hear them.