IMO, best and favorite will always or nearly always be the same. Because favorite is the one I enjoy playing the most, and the things that make me play it more are the very things that make it a better game. If it was just a discussion of game mechanics, then my favorite might not be the best, since, while I enjoy playing the game, there may be a game out there with better gameplay than my favorite. But when speaking of the game as a whole, everything goes in. Plot, characters, gameplay, subplots, love stories, boss battles... Everything. So, while FFVII may have what I consider to be the best ability system of the series (and it does, I love the Materia system), FFVII may fall short of being the best because that system doesn't make up for what it lacks in other areas. Thus, my favorite, the one I enjoy playing the most, will almost always be the one I consider to be the overall best. And I think you will find that nearly everyone thinks that way.
