What do some fans see as DS9's flaws?

Honestly, while I don't have an issue with the idea of S31, since any large interstellar polity needs a group that protects from the shadows. But, it was introduced at the worst possible time. And retconning it was a questionable idea... before DS9, it didn't exist. After, it popped up on Enterprise and Discovery and who knows where else, and its existence didn't seem to be that secret anymore.

 

But DS9 established that it was there from the very start of the Federation (at least, when assuming Sloan isn't lying about that). Can you really call it retconning in that case when shown in series that were made later than Ds9 (but play in an earlier era)? Or perhaps one should say that the retconning was done by DS9 by establishing that?

 

I think it would have been better done as a one off or maybe 2 parter, where Bashir is recruited, assigned a task or 2 and going double agent trying and failing to catch Sloan. Then when Sisko tries to log a report and asks questions about this so called "Section 31" gets stonewalled leaving us and the audience wondering what to make of it. Leaving the audience with more questions than answers and keeping S31 shrouded in mystery would have been better than literally going into Sloans mind etc etc.

As for later shows touching on it, it really ruins the top secret aspect of the organization but is also a commentary on how obsessed with such things our culture has become compared to even the late 1990s.

 

^Yes, I can understand how the later show bringing S31 as 'a public dirty secret ' could be construed as a retcon given that in DS9 it was portrayed as so ultra-secret that probably only a very few top-level admirals in Starfleet knew about it.

Of course, it can also be construed as the generation of Sisko and Picard being more naive about the Federation and partly believing the fairy-tale propaganda, whilst earlier generations were more accepting of the existence of and need for a 'dirty underbelly' of the Federation. Probably similar to how the generation that lived through WW2 probably was more cynical about how war 'should' be fought than we are today.