Vanguard. The secrecy behind the project is completely antithetical to the tenets of Starfleet and the Federation as shown in the television series, as are the lengths that Reyes and T'Prynn went to keep said secrets.
At least with Section 31, we know that the main characters think that they're wrong, and they don't (knowingly) help them with their misdeeds. With Vanguard, though, we have none of that; the "captain" and first officer are the ones fucking over a civilian--thousands, really, if you count the families of the Bombay crew who were actively lied to about the deceased's fates, but that pales in comparison to what they did to Pennington--just because they can.
Have you read
Reap the Whirlwind? A number of the points you make there are acknowledged -- and validated. I don't think
Star Trek: Vanguard actually advocates the choices being made by Reyes and Co. anymore than, say,
The Sopranos actually advocates membership in the Mafia.
I'm also not convinced by certain aspects of the Federation Council system as presented in Articles of the Federation; I would have hoped that they'd have avoided anything like the discriminatory Security Council setup (that reserves a chunk of the seats for those planets that just happened to be closer to Earth, and so were around at the time the Federation was created--I don't remember if they had the broader powers seen in the UN Security Council nowadays, though).
Every government we've seen in
Star Trek has broader powers than the United Nations Security Council, because the UN has no enforcement power -- it is wholly dependent upon the whims of its member states to get its will enforced. It would be more accurate to compare the Federation Security Council (name and allusion to membership rules aside) to the United States Senate Armed Services Committee than the United Nations Security Council.
In any event, I agree with you that it's fairly discriminatory to give the Founding Members greater representation than other Federation Member States, but it's also, I think, wholly realistic to expect that something like that could develop. For a similar example, to this day, residents of the District of Columbia do not receive full representation in the United States Congress, even though they outnumber the residents of the State of Wyoming! The original reasons for this were once valid; they no longer apply, but that doesn't mean it's easy to change things. The same is probably true of the Federation.
I also think that the method of handling a presidential resignation (or death?) is strange; rather than falling down a chain of succession, government more or less grinds to a halt until elections can be held. Doesn't seem very efficient to me.
Not really. The Council just appoints one of their own as President Pro Tempore. It's really not all that different from how many parliamentary governments handle succession.
What I didn't like about
Articles of the Federation was the idea that the Federation's highest court of appeals is not part of an independent judiciary, but instead just another Council committee.
But that is less problematic than the political system that was portrayed. I just found it impossible to accept the idea of a UFP spread across thousands of light years, with hundreds of planets, separated by years of travel time, choosing a system of government similar to 21st Century Western democracies, systems that barely work at the best of times now. Where was the input from Vulcan forms of government, Tellarite adversarial systems, and all the other governmental histories of Federation signatories?
Well, I think the thing to remember is that the thing that makes democracies so difficult to function is something that seems fairly universal across all of Trek's species: People disagree. Ergo, other species' experiences won't fix that basic flaw. Nothing can. And, really, nothing should.
The idea that there's a better system of government than liberal democracy, I think, is quite ludacris. Like Rousseau said, the people are the holders of political authority. Governments, as Jefferson wrote in the Declaration, derive their authority to govern from the consent of the populace over which they govern. Ergo, the only way you can verify that a government
has the consent of its populace is to ensure that the populace is an active part of that government: Voting. Democracy. No other kind of government can claim with any hint of logic that it derives its mandate from it's people's consent.