I was a huge fan of Metal Gear's lore until MGS4 happened. It was such a clusterfuck of idiotic conclusions to long-standing questions and overblown melodrama. However, I later gave Peace Walker a shot and it managed to renew my interest in the franchise. So I think no lore is beyond repair; rough times can be left behind as the game focuses on new, better though-out lore. Take Med'an for example, he was never retconned out of continuity, but as Blizz keeps on ignoring his existence he can do no damage. I also feel WoW's universe and its rules bend better to less savory lore-decisions than more "realistic" franchises like Metal Gear.