That said, I'm not so sure I want to. What I'm developing right now is basically a three-faced game. You can build an empire, you can oppose this as a sort of a force of nature, or you could be sort of a balancer who is a free agent. When you first enter the game, the map is replaced with this faction selection screen:
Of course, there's a lot one can do to beautify this, but it's a moot point now.
I did this because I could and it seemed novel. However, as I get closer to the finished results, I don't like it. It segregates the player's needlessly, it shorten the game's longevity by spreading the elements across the three factions, and forces them to throw away all their progress if they decide they're bored and would like to do something else.
I think I've got a better plan, borrowing some elements from X3 and (a game I tried for the first time this weekend) Majesty 2. Basically, I let the players start off as a pilots of single upgradable vehicles, but eventually they'll grow into roles of increased responsibility and power. As for our Natives/Aliens, they'll be more in the realm of being dynamic NPCs to take down - this has several advantages such as no longer needing to track an economy for them.
majesty 2 is to majesty 1 as star wars 1-3 is to 4-6
and yeah, starting off as a single upgradable vehicle seems like the best choice