I considered both gameplay and plot reboots in my list. (Star Fox, Star Fox 64, and Star Fox Zero are all versions of the same Lylat Wars)
I was not trying to define "reboot". Quite the opposite, I was just wondering what 4 Game Freak actually wanted, because Nintendo constantly resets both their series' plots and gameplay.
Does he want something drastic like Bomberman: Act Zero?
No, not to that level!
I just want them to go back to basics. Go back to what made series like Mario and Zelda popular in the first place.
Honestly, I liked the whole"Marios were Earthers from Brooklyn" story from NOA. Perhaps they could just use the original tale of how they first got into the Mushroom Kingdom and next. The story structure I would have taken would go like this.
SMB1/SMBLL > SMBUSA > SMB3 > SML1 > SML2 > SMW
This way, they could re-introduce us to the familiar characters and worlds in a much more proper way, as well as not overuse Bowser as much.
Let's also take Metroid. I want the gameplay and immersion to be as good as, at least, Super Metroid or Metroid Prime. As for Story Canon, its Structure could restart like this.
Metroid 1 > Metroid II > Metroid Prime
Because I kinda had some questions regarding Super Metroid(how did Mother Brain come back, for one).
I'll speak more of these at some later point.