Subcon
How did Bob-Ombs, Shy Guys, and Snifits get theirselves into the real world? Super Mario Brothers 2(Western version) tells us that Sub Cons and their world were both dreamed up by Mario. You'll recall Shy Guys and Bob-Ombs made an appearance in Super Mario World 2: Yoshi's Island and Yoshi Story, both before Super Mario Brothers 2 chronologically. Could Mario have included them in his dream as if it were a nightmare? This could also explain the Bob-Ombs' change in look--don't things look a little different in a dream? And, obviously, those past enemies still exist today.

Items
Last time I touched a flower, I didn't don red overalls and a white shirt and cap. Maybe something happens, like an alergic reaction of some sort, that gives the brothers the power to shoot fire or fly or whatever the item might do. Then it might react to the fabric of our heroes' clothing and change their color.
In the case of Extra Marios and Luigis, I don't believe there are any. When the Mario bros snatch a 1-Up Mushroom or 3-Up Moon, it gives them nothing. They don't come into play until later, when the brothers supposedly die. They just run out of energy, and then the items kick in to reenergize them. By the time Mario and Luigi are concious again, enemies have dragged them to the beginning of the stage, or the journey if there is nothing to help them. The life counter shows how much energy one of the brothers have left.

From Brooklyn
American influences(the cartoons, the movie, the computer version of Mario is Missing...) give Mario and Luigi a hometown of Brooklyn. The movie and the cartoons conflict on this thought. Super Mario Brothers the movie put Mario and Luigi in the Mushroom Kingdom through a portal, although they don't stay. In the Super Mario Brothers Super Show the brothers fall in through a tub's drain. Most likely the movie happened first, then the cartoon. But how did they move so far so fast both times? They could have been broken down and rebuilt in the Mushroom Kingdom. The atoms weren't moved, but replaced instantly in another place in the universe. Or, the Mushroom Kingdom could be on a masked place not discovered yet on Earth, and the Mario bros passed very quickly through piping.

Baby Mario and Adult Mario, DK Jr. '80's and DK 90's/00's
Mario Tennis 64 tossed Baby Mario and DK Jr. in with their elders, or rather, their future selves. Remember those portals that took the brothers to the Mushroom Kingdom? They also might take people through time and not just space. The two youngsters could have wandered in and found themselves there.

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