I now headcanon Kamek and Kammy are Bowser's adoptive parents
which also means I headcanon there's a 3D Kammy and a Paper Kamek
And that Wario & Waluigi's relation to Mario & Luigi is that they're Corrupted (through dark magic ztar stuff) Humans and were named accordingly. And that Bowser/Koopalings are corrupted Yoshis.
To go farther into this, I headcanon Kamek & Kammy stole a baby yoshi, possibly while still unhatched, and corrupted it with magic/ztar energy, raised it as a "Prince" to "take the thrown as King" basically as Koopa's ultimate Warrior. I headcanon the Magikoopa's are the true rulers of Bowser/Koopa Kingdom, and *try* to use bowser as a puppet (but the older bowser got, the less control they had over him, eventually he really does become the ruler).
I also think somewhere down the line of things, they also corrupted 2 baby humans at the Stork Hospital, but they didn't know which humans were the corrupt ones, so they kidnapped everyone from the hospital (Baby Waluigi got delivered late because he wanted to finish watching cartoons). Yoshi's sabotaged their plans to raise corrupt humans as warriors for their army and brought the humans to their appropriate homes. Wario of course led a life of his own, the koopa's could not control him at any post encounter.
WHICH LEADS ME TO THE FINALE OF MY HEADCANON
Why we never see Waluigi in canon/adventure games? After Kamek failed to abduct the other babies, he saw the Stork come by again, he knew it was 1 of the babies he missed, and nabbed Waluigi from the stork. No one knew, the magikoopas have been raising Waluigi and training him to be the biggest baddest boss in secret. He uses magic/zstar energy, he's not supposed to let people know too much about him, but he's revealed that he can turn ground into water and swim through it, and that he can create tornadoes.. I believe that's a small percentage of his power.. someday it will all be revealed and he will be the final boss, as the leader of the magikoopa guild.