Actually, if the 4th race could be a menagerie, that would be cool. For instance, a Gorn ship or two (true to the one encountered by 1701), a planet killer, a mirror universe Enterprise or some Fed ships taken over by the M5 computer, a tholian, an organian (bright ball of light, as strong as a cube), mudd's pirate cruiser, Cireno Jones' cruiser (with TRIBBLES AS CARGO)
, lazarus' ship from the alternative factor, an energy cloud like in Metamorphosis, an actual model of the Nomad probe(?), in The Immunity Syndrome an enormous space-dwelling amoeba, Khan's Botnay Bay, and ... this would be SO kitch--- a huge hand of apollo that locks you into a non-repellable tractor beam and crushes your hull
Also, all the Fed bases look like space station K7, and we should have one mission where the player's ship takes damage from a computer-generated war, as in A Taste of Armageddon.
There is precedent for a Daedelus-class ship to show up (A Piece of the Action).