Another vote for Rise of Nations, the series, great game!!!
Homeworld, expansion, and part 2, great stories!
Also, these are pretty old school, but Earth 2150 is good, it had a part 2 game but I never played it. I'm not sure the title of this next one but it dealt with MARS, you were either human or alien and it was a pretty fun rts. I think it was called MARS, i forget, like i said, pretty old school 97' i think, all I know is it came with my compaq computer back in the day when it cost $3,000
edit: Also Age of Mythology! how can i forget this game. Another good game with a story involved