See, initially I liked to think that there were two "main universes":
-The one that was largely made up of classic games, where Bowser had the Koopalings, the Mario Bros. came from Brooklyn, Yoshi's are animalistic, Bowser's minions are really dumb, Mario got his hands on a castle, and Wario was an evil villain
-The one where all the newer games are placed, where Mario and Luigi were born in the Mushroom Kingdom, Bowser has only one son, most creatures possess human intellegence, Mario is always living in a house, and Wario is a greedy slob (and has a brother).
Get it? That's how I wanted to explain all the differences.
Also, minor titles which would ordinarily be deemed "non-canon" by some due to all the inconsistencies and whatno would be considered multiversal crossovers.
Then I got the idea to separate games where Mario takes on a completely different role into universes of their own. I started with Dr. Mario, then moved on to things like Yoshi's Cookie.
One last thing I aimed to rectify was Rare's portayal of DK, but I haven't gotten around to that. I was thinking that the "old" universe would have the "classic" style DK, along with DK Jr., while the "new" universe would have Rare's DK, along with other DKC characters. However, there's still the matter of Cranky...