Here's one idea for a possible origin of worlds for the NCU that I came up with, which works with all of your ideas. Before I begin, my notion for Luigi to be evil is based off of the game Super Paper Mario, which is an amazing, enjoyable game.
The NCU begins with infinite earths - akin to many different things, such as DC Comics - with each having separate lore. Across Phase One of the story, the heroes are separate and have fun stories with their respective casts, but all notice R.O.B.s building complicated machines in their world. (The Subspace Bombs) They let the R.O.B.s do their thing, because they seem harmless. At a later time, each world suffers from an invasion by mysterious creatures, and the main heroes are whisked away to the Grand Stadium, where Master Hand tests their fighting. Some heroes (ie: Luigi) can be corrupted by the Subspace Creatures. The heroes try (and fail) to stop the bombs from going off. After they loose, their worlds are consumed by the bombs - which moves their worlds through space-time, so that they are all right next to each other. Master Hand reveals he is a good guy.
Does this make sense?