I'd like to see minors be able to join your empire in a federation type system. They can stay autonomous, controlling their own planet, but produce units, research etc for you. They could be indirectly controlled through a governor/senator which Frogboy wanted to implement in the game, and sort of like puppet-states in CiV. In fact this could be expanded for your other planet: each sector governor controls a few planets depending on your political system. Having different shades of your influence colour could also add some interesting graphical flare to a federative political system. Of course this being a game you might also need to be able to take control of a planet and order it directly what to do (unless it was a former minor).
But year, minors now are a bit annoying, always asking for things they can't enforce.