Personally, I think that you should have a threshold, where, rather than all aliens being able to rank up to colonel, aliens have a starting rank based on their species. So Vipers and MECs would be Squaddie aliens, but Mutons would be around Sergeant Rank, and Andromedons at around Captain or so when they are added, with Sectopods being 2 soldiers slots in the avenger (-1 squad size, basically) and a starting rank of colonel, as... well... they're Sectopods.