Before I go into any differences, I first want to make note that in most of the games where the protag you don’t play is does not appear, or only appears minimally (BW, BW2, SuMo, SwSh), I have both protags as “canon”, each sharing story elements. For example, in Galar, both Victor and Gloria compete in the League Tournament, and Victor becomes Champion and goes through the Crown Tundra DLC, but Gloria is the one who has the more significant rivalry with Hop and goes through the Isle of Armor DLC. For those games, I consider both protags canon, so my ships wouldn’t change. I also consider Red and Chase to be the “canon” protags of their respective games in this AU, so their families would also remain the same.
That leaves us with: Ethan, Brendan, Lucas and Calem.
I think the only one of them who’d have a different family is Ethan, who would be endgame with Silver this time, while Lyra would likely end up with just Whitney (as the way I hc her personality she’s less likely to have the same kind of admiration of/relationship with Lance that Ethan does). I’m not sure how their kids would differ, but I am (very slowly in the background, not likely to see light of day anytime soon) working on an alt-L&L verse with different ships where Ethan/Silver are endgame, so I might have some ideas eventually!
Brendan, Lucas and Calem would all end up with the same partners (Wally, Barry and Serena), their initial dynamics would just be a bit different. I don’t think their families would be too different in the end though, though perhaps some of their kids might have different interests – Gavin might be a trainer instead of a researcher if protag!Lucas is the Champion rather than a Professor, for example.