Case by case means who has the most political pull inside of the NFL. The New Jersey Super Bowl is in a stadium that is host to two NFL franchises. Personally I think it sucks that they did away with the "no Stadium that could possibly have in-climate whether conditions would host a Superbowl."
When I watch a Super Bowl I want both teams to be fighting each and not the weather. Such a game skews towards a cold weather team if it goes up against a warm weather team. That kind of does away with the idea of the game being played in a neutral site if both a warm weather team and a cold weather team meat in a cold weather Super Bowl.