Having been denied the opportunity to raise his own daughter, Troubleshoes is more than delighted to be part of his grandbaby Pepper's life. He even moves to Manehattan to be near his true family. Here he is having a trot-about with said grandkid, who's pretty sure she can get them both off the ground if she holds on tight enough with her little hind hooves.

Even as a young baby-type foal, Pepper is a big strong kid with even bigger-strong wings. I venture to believe she's often mistaken for Mama Babs's biological offspring, which I'm sure pleases them both. As for Shoes, his mighty half-earth-pony, half-Clydesdale genes explain a thing or two about Babs's especially-big-strongness. She's a quarter-horse. See what I've done there? Hyphenated words, I've got them!

mlp:fim = Hasbro/Faust

Tldr: In Froggie's JG universe, Troubleshoes is the long-lost but ultimately loving father of Babs Seed. Sweet Pepper is the adoptive daughter of Babs and her little nerd-wife Twist. We are fam-uh-lee, come on everypony and see.