I would not mind to see a very darker federation. The problem I see it, most have talked about issues that would be very limited and would come to an end the first season. If it is going to be darker then even DS9, it would not be thought a good series unless it last the stardard time of 7 seasons. If they come up with a new series that last as long as Enterprise, it would be thought a second and final flop.
Maybe something dealing with a federation civil war, and ending a a war or as close as it can get. Still, it has to have some positive with it. Like to get people interested, like the first same sex marriage in a star trek show or a movie. People in science fiction like the dark side, but it cannot always be about the darkness.