I think Michael got a great story and his character really worked towards it. The conflicts he has put himself under, despite how long he has tried to fix them, keep coming back and it nearly destroys his family. I think he's one of the best protagonists in Grand Theft Auto.
For Trevor, he also got a very good story and in my opinion, he got the best characterization of all three of the protagonists in the story. I at first was wary of him just being a one-dimensional psychopath, but my doubts were dashed midway into the story.
Now onto Franklin... he's not a terrible protagonist, but he is my least used one. It's not that his story is terrible, I believe that it was the way Rockstar gave little of a good story to go on for him, and his character ended up suffering from it.