Here's some more ideas, some taken from my own Civ 2 scenario:
http://underworld.fortunecity.com/mario/92/
(Wow it's still there)
I don't really know how you're planning to do the terrain- is it all going to be land, with space representing a no-go area for units?
Anyway, some recources:
-Spaceborne organisms
-Antimatter
-Dark matter
-Hytritium
-Plasma
-Tritanium
How's the workmhole going to work in specific scenarios? Perhaps have a long chain of terrain going across the quadrants, but make it inpassable, with railroads on it, which would mean it's only accessible to whomever owns the entrance, and then connect it to passable terrain at the other end; I'm not sure if that will work, but it's something.
You've left out the Cardassians' Hideki class ships, which are probably the only Cardassian ship other than the Galor class to be identifiable in an actual episode of Star Trek (They're quite evident when the Dominion captures DS9, one seems to explode on the station's shields, also in the Sacrifice of Angels when a number of ships break from formation to go after Federation fighters); look here:
http://www.neutralzone.de/database/Alien/Alpha/CardassianHideki.htm
Some wonders, may be a bit race-specific:
-Daystrom Institute, best used as a science wonder;
-The Prophets, pretty obviously a replacement for the Oracle, but may act as a more general happiness wonder;
-Starfleet Academy, but might be a bit extraneous;
-The Obsidian Order;
-Sword of Kahless;
-Artifical Peoples' Suffrage, to give Androids and Holograms equal rights, replacing universal suffrage of course;
-Janeway's Voyage;
-Vidiian Medical Treatment, dunno about this one, maybe give it to the Kazon, make the Phage a very rare resource that you need to build it.
Okay that'll do.