I was more thinking you'd add traits as you progressed rather than replace them. OTOH, perhaps you'd add one at the start based on what tech you researched first, then later you'd add two but take one away. This would sort of force you to change your strategy as you went along, because you'd have to stop being something, but you'd want to rush through as much as you could to make the net-gain.
At the very start of your post, you put me in mind of Black and White 2, and the way in which your pet develops its abilities and personality based on your actions. Frex, I train my pet not to attack my stuff, but to attack other people's stuff. I give him plenty of combat ability (I didn't know he would respawn if he died, and I didn't want to lose him, until I'd played a couple games). But alternately, I could've turned him into a production assistant, or a morale booster, or an army helper (healer), or any number of other things, and that's the first impression I got, and read wondering how you'd accomplish this.
In answer to my own question, I don't know. Maybe implement some kind of morality choice system, not unlike what's present in GalCiv2.