just take the storylines from the Original Marios... I have never heard of M&L and never played any of Paper Marios but in the original 3, Mario and Luigi are from NYC and got lost in a pipe that took them to the MK. This is also in a book made about Mario from Nintendo Power. At the same time the marios appeared, Peach is kidnapped with her toads... The mario brothers where first helped out by Peach before she was kidnapped and went to work for her as plumbers. After hearing of the kidnapping they feel bad and go to her aid thus initiating SMB 1,2,3 etc. They want to get home but are not sure. I am assuming Pauline found the pipe eventually and came through.
The old Kong (I think Cranky) from the DKC series is DK from the Arcade not the DK from DKC. DK jr was DK's dad from DKC. I am assuming that the DKs followed Mario through or that they have there own world and came to brooklyn then found there way back to MK.
I want to see Wart again though and I think Nintendo messed up to not use Characters from SMB2 again and also to get rid of the 7 bowser children from SMB3 for Bowser Jr. They should make a new Mario game with DK and his crew in it that has Wario, Waluigi, Bowser, King K Rool, and Wart all as enemy bosses. Have DK as a boss that when you beat him he becomes playable. Make it 4 player with Diddy Kong, Yoshi, Kirby, Mario, Luigi, Toad, and DK as playable. (make DK, Diddy, and Kirby unlockable when you beat there stages).