Why the Baby Bros. are the current Mario Bros.

Interesting.

Although I think they may have also recognized Popple and Fawful, but did not show it in case someone is new to the series and doesn't get it. They didn't give too much detail about the Shroobs, other than "defeated when they were babies" so it wouldn't be as confusing; a newcomer would think "So these things lived in Mario & Luigi's past. Interesting" whereas with Fawful or Popple, they are actual characters rather than the Shroobs who were just generic ones (probably why they didn't add Princess Shroob to the mix)

But I get your theory; it's pretty mind-boggling. You should also post this topic on the MarioBoards; it really is interesting.

Well, It's just a theory, a Mario Game Theory.

I found something: I am about to fight the shroobs in BIS, and Mario and Luigi are scared of them. Mario explained what was going on to starlow. Mario said they were aliens that once invaded mushroom kingdom, and that they defeated them when they were baby's.

I have another piece to add: Bowser did not recognize Fawful in BIS, even though he was severely crippled due to Fawful in Superstar Saga.