In my “head canon” we are indeed in the Mirror Universe, and the “good Federation” is on the other side of the mirror.
That said, while there’s no denying that Trek is now darker in general, there have always been stories about dark forces and bad people within the Federation too. A rogue Starfleet captain somehow turning a whole planet into Nazis comes to mind, but that’s far from the only example.
Maybe the point was that a utopian, post-scarcity society is well and good, but even such a society will have its criminals, bigots, megalomaniacs, etc. Making the human race solely a force for good is a constant struggle and a worthy goal, but not an achievable end state.
That may not be quite what Roddenberry had in mind, but I think it’s more or less necessary to make watchable drama that isn’t just the Good Deed of the Week.
Does newer Trek take the darkness too far? I don’t know. My objection to the Abrams movies is that they’re shitty and utterly unnecessary. (Marking myself as an old curmudgeon, because I also know these movies had some success in bringing younger fans into the fold.)
My objection to Discovery is mostly that it’s very silly and all around ill-advised as a prequel to TOS.
After two episodes, I don’t have a solid opinion on Picard. I think there’s room for it to have an optimistic perspective overall, but that remains to be seen. Until we find out, I won’t be surprised that it’s also loaded with 21st century action-movie tropes.
