The story isn't so much weak as underdeveloped. It just doesn't bother to adequately foreshadow events or develop characters. What actually happens in the course of the campaign is alright, and the scripted missions themselves are pretty good. Anyway, it doesn't matter in an RTS, and there have been far worse stories.
On that note, anyone know if there's different endings based on the choice you make at the beginning of the Cuotl campaign?