I think the current mechanic is fine, we just need to have a few more options. If we could set the allegiance of any group, that would be great. Also, if we could have separate Cardassian and Jem'Hadar ship groups. And if we had "boss" groups, which were just a single ship (Frigate/Cruiser/Battleship/Dreadnought) that was scaled up to be difficult, then I think we'd be good.

I think the only issue with the contacts is the contact limit needs to be doubled.