I think they could have used Miles way more. Like at the end of season 4 when him, Calire, and Sawyer are making their way back to beach he has that line asking Claire if she's "sure she's ok". And when he kinda looked like he knew something was up with Sayid. They probably could have used his character to move those parts of the story along more. Plus, he's awesome; so they should have used him more just because of that. Out of all the freighter people Faraday was the only real important one.