Universe against universe itself seems stupid, but it makes for completely new FS2 (FS3???? ;-) ) missions ...
F1: Mayday, mayday. They are following me.
Ross 128: Calm down pilot. We had that whole story already. Was it vasudans?
F1: They slaughtered everyone.
Ross 128 (bored voice): Was it shivans, terrans, hybrids, vasudans, HoL, NTF, NNTF, NNNTF, a plane?
F1: It it it were ...
Ross 128: What pilot?
F1: Send fighters! Uh no its too late ...
Ross 128: Pilot, pilot!
F1: They are CATS!
... Marketing Voice from Off: Yes, really nice kitten. Everyone ought to have one, visit kittenwar.com now ;-).
Anyway joking aside, I think you don't have to balance out the universe from start up. when the shivans first arrived, the GTVA was also not balanced to them.
Then you can create hybrid craft with the help of the technology of the new enemy and balance up to it ... or die

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cu
Fabian