One thing I would have done with this film is to leave the story basically as it is, but do something that Nolan did in the Dark Knight
, and that is to give nearly equal time to the various philosophies, so that we can see them all at play and decide for ourselves.
Int the Dark Knight
, there is almost equal time getting us to understand the different philosophies of the characters and where thy stand on the morality scale.. and I'm talking about Batman/Bruce Wayne, Joker, Dent, Gordon. Each of these characters is given a moment in which their ideologies are placed at the forefront. They are each given equal footing.
, Section 31 is a very important element to the story, an yet for some reason, they are almost a passing reference tossed aside. Why not give the viewer some insight as to what they are about, a little more detail about how they have and can continue to protect the Federation. We might not ultimately agree with their vision for a more militarized Starfleet, but that doesn't mean that the writers can't make a good case for it. We don't agree with the Joker, necessarily, but his ideas feel ultimately convincing, or, close to it. that's why he's such a good adversary. I think Section 31's role could have been fleshed out and defended, and so could all of the other viewpoints.
Even with all the plotholes that would still remain, it would make this story one that peopel will remember fondly.