We could turn into another tech sub-tree. You first have to research alien light armor to get to medium and then on to heavy, so that if you managed to take down a boss with heavy armor, but havent found light armor, theres nothing you can do with that armor until a later point in the game.
I persionally really like the ideas of bosses or field commanders, though they shouldnt be on every mission. And it would be easy to make them stand out, if thats what we are aiming for (thought I think it would be a much better idea if the "commander" blended in with the rest of the aliens) by simply making it a different size along with different textures, beyond color changes. Put some markings on its head, some decorations on its clothing/armor. When we are just playing with images, we just need someone with talent to add the small changes