Hard to compare the two... two different styles of games. The franchises on the other hand, MGS has done much better than FF in terms of enjoyment in each subsequent sequel (for me anyway). MGS keeps getting better with each sequel whereas Final Fantasy seems to have gone downhill since VIII, each sequel moving further and further away from what the series once was. VI was the peak of the series for me, I was really disappointed with VII, VIII put my faith back in the series, but IX, X, X-2... I just couldn't enjoy them like I did the others, and they kept getting worse and worse.
Back on the topic of Retro games, I still love Zelda: A Link to the Past. I actually pull it out once in a while and give it a play though.