I think that the Jotunheim and the Andromeda especially will get along well, given their tendency for more "traditional" battleship-shaped cruisers, their use of small space fighters and their fondness of Wave Motion armaments and technology. Technically, there is a nearly a century of time difference between the rollout of each ship, but who cares?

Generally, I think player cooperation with the Trekkies are what will give the player fleet a key edge.