By the time of TNG, the Federation spans 8000ly has over 150 members, it's population could be in the region of hundreds of billions if not close to a trillon. Now witha population that vast there are going to be some people who have certain flaws, just as today. But by and large like today they seem to be in the minority.
As for the issues regarding the PD, they are damned if they do and damned if they don't. Some people would argue today that the Western Nations(esp: the USA) should keep it's nose out of there affairs).
As for the Maquis, the inferrence from TNG when planets swapped and the population choose not to be relocated, was so long as they didn't bother the Cardassians they would be left alone. The fact that the Cardassians choose to ignore that or certain colonists start causing trouble is a different issue. At the end of they CHOOSED to live under Cardassian rule. Now you can argue forced relocation etc.., but at the end of the day the Federation has to do wghat is considered best for it's entire population. So the new borders and the DMZ that came about with the Cardassian treaty, if it hadn't been signed it could have led to another war, costing who knows how many lives all so a few colonists could stay where they were. It comes down to numbers at the end of the day.
So what if the Federation hopes that one day the Cardassians/Klingons/Romulans etc.. will join one day. Thats a dream of a better tomorrow where we live in peace withut threat of war. They aren't forcing them to join, they didn't say join us before you can have the replicators.