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The real way to go forward as a franchise would be to either bring back spinoffs, or go the Mario and Zelda approach of having multiple different types of "main series". Majora's Mask and A Link Between Worlds are incredibly different, but are still a part of the main Zelda games. You don't need to get rid of GF's games if the sequential approach helps with making new Pokemon and toys, but there could still be an opportunity to make games by different groups. Having multiple different styles of games could appeal to different groups of people and get certain people disinterested in the games into it without alienating others.
Also worth noting that it's been five years since the last Mystery Dungeon, and that Ranger, Orre and Conquest are just as dead.