The Federation (and Star Trek) has entered some fairly morally questionable area's on the part of the Federation, so I interpret the Federation as a Bright, But Flawed, look at the Future. This is due to a lot of the rather Tone Deaf writing of some of the writing staff trying to gin-up 'Drama' including but not limited to:
1) A.I. Is A Crapshoot. Yeah, Artifical Intelligence tends to get the short end of the stick in Trek, but then most A.I. seems to follow the Berzerker/Terminator model or dumb as a rock servant. There apparently is NO in between in Trek. Which I find really truncated and stupid. LEt's see some actual smart frames or artificial intelligence that is actually helpful developed as characters. It would make things more interesting. And the Treatment of Photonic Lifeforms is appalling by The Federation, who seems to be okay with slaves that do not bleed.
2) All Hail the Federation....even when they are being complete jerks to you. TOS, which perhaps a bit cheesy on some of it's speechifying, did not get too heavy handed...usually. TNG and particularly VOY suffered from and I really hate to say this "Great White Man come to enlighten the natives." Seasons one and two of TNG were particularly bad in this regard, but thankfully they dialed that back a LOT. The less said of Voyager the better. To fix this tendency, I'd like to see the new crew come across a problem, figure out how to fix in and then soft sell it to the people they are interacting with through understatement and simply stating politely, "This is how we do things." Leaving the contact of the week to think about what they have seen and follow up with politely answering questions, not rendering any judgement unless asked. This would be closer to a more mature set of Federation officers which is kinda playing on Gene's 'Evolved' nonsense.
3) No Genetic Engineering: Okay, seriously. The Augments and the Eugenics Wars were from over 400 years ago. Get over it and yourselves, Humanity. It would be interesting to see other human variants that had not followed the genetic restrictions having built local coalitions that the Terrans would have to deal with or be proven hypocrites. Let's see if that 'Utopia' stands up under scrutiny. there was a novel about a colony of Augments that did not want to interact with the Federation as they heard the horror stories from their ancestors, who were early Augments (think Khan and his Ilk) who they considered nutters, but understandably so. The New Augments were a significantly improved version of the regular augment version, but had certain genetic modifications to make them more stable and personable. They would probably make great Federation citizens, if the Federation wasn't a pack of lunatics form their POV. The commentary result was hilarious, pointing out the obvious flaws in Federation logic with regards to genetic engineering.
4) Section 31: I had no problem with this showed up in the show. I expected there would be an Intelligence Office around somewhere that kept track of all of the hostile empires surrounding the Federation that worked with Starfleet's Tactical & Strategic office. I also expected there to be a Black bag operation somewhere handling the things the Federation would rather not acknowledge. The fact that it is literally off the grid with no official status or registry, makes it devilishly hard to spot by OpFors and more effective in the deniability area. Where the execution of the idea fell down was that A) distinctive black leather uniforms....that looked horrible and what moron thought those were a good idea? B) s-31 agents should exhaust every other option reasonably before going for what I call the "Bastard Option', but if they have to, just set it in motion and tell the minimal amount of information needed to let people wonder what just happened. And plans within plans within plans to make them effective. IDW's Star Trek Series portrayed S-31 as quiet, manipulative and capable of carrying out contingencies that played the Klingon Empire AND the Romulans like a fiddle. No more of this Federation nativity nonsense. If you are going to have this, then make it a credible threat
If they kept this, but made these tweaks, it would open up more plot ideas for debate and a bit of a fresh look at older subjects
A brave little theory, and actually quite coherent for a system of five or seven dimensions -- if only we lived in one.
Academician Prokhor Zakharov, "Now We Are Alone"