Here's my take on it:
Far Cry 3 is one of the best games from the last couple of years, truly brilliant. From a psychological standpoint, you relating to the character is absolutely understandable. At it's core, it's about a young man who feels weak and inferior (particularly in comparison to his war hero older brother), finding this inner strength he didn't know he was there, and being forced to push himself to his physical and mental limits. It's an awesome journey, and it's how we all hope we would react to the circumstances.
That said, you do find yourself in situations within the game where the character is forced to do some truly questionable things. I approach any game I play with Christ in mind. I want to know and understand a character's motivations, and if I don't like what he's doing, or why he's doing it, I back off. Far Cry 3 is unique in that, while you're not always doing "good" things 100% of the time, it's all coming from a pure place, and much of it is a result of circumstance beyond the character's control. Ultimately, you're trying to rescue friends and family, and one of the side results of that journey is bringing down an organization of brutal murderous pirates, and basically destroying a major drug operation. There are also plenty of opportunities to help out locals and natives by doing a good deed here and there, all in all, there are worse characters you could model yourself after. However, do keep Christ in mind in whatever choices you decide to make. Physical fitness is awesome, great for body, mind, and soul, plus it's good to put down the controller once in a while. I take breaks and hit the home gym as often as I can. Traveling will also do wonders for the spirit, and I agree with the person who suggested making a mission trip out of it, it would be an amazing and rewarding experience on all counts. The most important thing to remember, though, is to glorify God above all.