Nintendo needs to make a game that explains the rift in the time space continuum. I personally think a toad with evil intensions got ahold of E.Gadd's time machines and went around messing up events in the super mario time-line.
The toad responsible happens to be a toad found all the way back in SMB that said, " sorry mario, our princess is in another castle". He somehow felt mistreated by mario and went rogue. Maybe he is in control of all the many villans that kidnapped Peach in the past, the toad happens to be the mastermind behind it all and bowser, fawful, smithy and any other bad guy you can think of are just puppets of this toad.
Nintnedo could make a game where mario revisits parts of his old games to repair the timeline.
Because it would have to be someone with inside knowledge of the castle(peaches) and mario's exploits. Not only that, but it would be completely unexpected and out-of-left-feild. The toads name would have to be somthing sinister like Toad-laden or Toadler or Toadithy Mcvey or Toadam Husein..... you get the idea.