I don't see Big Boss as a villain. I see him as an anti-hero. All his motives and actions have been to promote the worth that he felt that soldiers deserved, and he is also seen as a savior and father figure to several MGS characters. It's just like The Boss says in the end of MGS3, who the badguy is depends on the world's current situation and what needs to be done.

Which is also perhaps the best part of Metal Gear's overall plot, in my opinion.

I also want to add that I've beaten MGS3 many times and tears still fall during the ending, especially when Big Boss does the salute in front of Boss' gravestone. [img]i/expressions/face-icon-small-sad.gif[/img]