Well the Nintendo franchises are typically: 1. design a game. 2. make sure it plays very well. 3. make up a story.
That can go on forever.
Metal Gear has already covered the present, the future, the past, the past again, and the future. Too many more trips to the past/future, and Marty McFly is going to have to come in and reboot the whole franchise. It's a great series (probably my favorite) but it has to end.
Would've been a tougher choice if Metal Gear was left out.