The problem with crossing shows is that you have to make up a middle ground or one will mow down the others. When someone did a Babylon 5 vs Star Trek aniamtion, they took away shielding because they knew that ST:TNG would tear through Babylon 5 tech. By the same token, I think Eve would jack up Star Trek, Star Trek would come out just ahead of Star Wars, Star Wars would beat out Babylon 5, Babylon 5 would be fair competition for Freespace. Homeworld would be in the middle as they have impressive offensive capabilities and numbers, but lack defense, which tehy make up for with great variety (more in Homeworld and Cataclysm than in Homeworld2).
So if it's a matter of them taking on everyone, feel free to play with it as nothing can be true to the original and still be fun to play.
Oh, and you don't have to worry about adding those races. Other than the Taiidani and Somtaaw Kiith, most were support roles.