An easy variant to incorporate is giving players multiple aliens in the game, allowing them to take advantage of multiple powers. Below are just a few methods for employing multiple powers.
Planet Assignments - Place your alien cards next to each other, and then assign planets to each alien by placing them on the outside of the aliens. The planets to the left of your left alien are associated with that alien, and when you are on defense, you can only use that alien when those planets are attacked. The same is true for the planets on the right side of your right alien. You only lose control of an alien when you have lost all of it's assigned planets.
Example: Let's say I have the Mirror and the Clone as a pair of powers. I lay them next to each other (Clone on left, Mirror on right). During setup, I decide I like the Clone better if I only have one power, so I put 4 of my planets next to (left of) it, and one planet next to (right of) the Mirror. If I lose control of the one planet associated with the Mirror, then I lose control of that alien power. But if I lose control of the other 4 planets instead, I lose control of the Clone. Of course, you might make the rules a little closer to official by saying only 3 planets can be tied to any one alien power, but the point is that this could add some strategy to the planets being attacked, and make it less likely that a player loses all of their powers.
oooo|Clone | Mirror|o
Lose use of Clone:
xxxx|Clone | Mirror|o
Lose use of Mirror:
oooo|Clone | Mirror|x
Lose use of both:
xxxx|Clone | Mirror|x
In this setup, cards or powers that depended on the number of tokens on your home planets would count all the planets, not just the planets next to the power (otherwise, you screw up the design of the power or planet).