A stopgap solution might be to have the envy penalty by limited by reputation to some degree, so only empires who misbehave get the whole galaxy hating on them. Whereas if you keep your nose clean you can overcome the envy with gifts and trade etc.

It is the same issue with independent planets being so easy to colonize versus invade: gift-giving is mad strong and not expensive, just a minor outlay of cash to bypass any challenge.

IMO NAPing pirates / colonizing indies should require at least 2-3 techs from that species' diplomacy tree, so it ...

Spoilers I guess?

I had the Way of the Ancients quest trigger on an Securan world I had colonized early on. I sent my leader to investigate, then got the popup telling me he'd converted to the new philosophy, and that I had unlocked the new government type and could have a revolution to switch to ...