Fair point, RTS games are great at becoming a story as you play. I doubt you will find many people here who would disagree with you.
After all, we all enjoy AI War, which is emergent gameplay at its best.
Red Alert might have been a bad example of a game telling a story, I just love its cinematics, it was a biased choice.
All I really wanted to say, is that RTS games can have a story, it is not playing to the genre's strengths, but it certainly can be done.
Hopefully, without relying on cinematics, but somehow, creatively sneaking it into the gameplay.
I always liked the campaign missions in which you are limited to but a few units, it transforms the game into a sort of a puzzle to solve. I'm sure there are some fun ways of putting constraints on the gameplay to suddenly change the player's experience. Though I'm not suggesting anything like that to be done to AI War, that was just a general remark on my part.