Roman Bellic. There's a lot of people who found him annoying, but I enjoyed my time around him during certain missions and thought he had a sort of innocent charm. Well... about as innocent as you get when you're caught up in gang activities.
James Vega from ME3. Much like the protagonists from Far Cry 3, everyone likes to mentally avoid Vega because of his appearance as a douche. But to me that's exactly what makes him great. Everyone seems to think that all characters should be likable and appeal to them. If you look past his appearance, you'll see that he has a meaningful background and emotions and stuff. Many just labelled him douche, but I thought of him as more of an action-loving goofball.
Initially, I was sorta put off by Nathan Drake's movie star action man persona. Then, after some internet discussion, it was pointed out that he was actually insane. Think about it. No authorities on his treasure hunting quests, millions of bad guys killed, and all the while, he acts cool and collected. It doesn't bother him at all. He's enjoying it. And that's awesome to find that underneath his initial appearance.