I always have the problem that the factions in my universe .
Always drift in to one being good (the Commonwealth) and the other being evil (the Collective or the Cthuhi)
For some reason my universes drift in to that black and white territory .
Any advice how I can add some shades of gray ?
Thank you for your time and patience .

I'm not thinking about "good guys" or "bad guys". There are different factions, with different ideologies. The Empire is not "Evil", but neither is it "good". the same goes for the Republic. Players should face an interesting choice when dealing with factions; having one clearly evil and the other clearly good makes this choice too easy.

Also note that, by default, this setting is intended for smugglers, pirates, mercenaries and various outlaw types, so most governments, regardless of politics, could be easily cast into the role of adversaries. After all, the epitome of this campaign would be the PCs found their own empire and thus opposing the others...

Did you ever think about making your space empires the good guys.
And the republicans and technocrats the bad guys.