I’m OK with some dystopia in Star Trek. I just don’t want it to be at the heart of the Federation and in an officially sanctioned way.
If Section 31 was some kind of conspiracy to undermine the Federation, that would probably be OK. It’s the idea that some top-level Starfleet officials created Section 31 and subsequent top-level officials have continued to sanction its activities for over a century is what I don’t like.
One thing I’ll note: there didn’t appear to be any Section 31 elements on the far-future Starfleet as seen in the later seasons of Discovery.
While it was sad to see the Federation in a diminished form, one thing I liked about those seasons was the hopeful rebuilding of the Federation to be a genuine force for good in the Galaxy again.