This is a pretty difficult question since for generally my “favorite” family is the one I’m working the most on at any given time, so the answer would change. I can answer for who I’m enjoying working on the most at this point in time though.
Kanto: I haven’t really worked in depth on any Kanto families recently, but I’d say right now I’m feeling very fond of the NamelessShipping fam. I’ve been having a lot of fun with Roy and Sage’s dynamic in particular, as antagonistic siblings is always fun. I also like how they both have some of Green’s arrogance, since cocky characters are fun to work with.
Johto: Hands down the HonorShipping family just since they have so much drama. A very close second is Whitney, Ethan, and Lance’s family, since there’s a lot of fun dynamics going on there as well. I think the sheer outrageous soap-opera levels of drama in the former family are what make me like it more though, as well as how quirky all the kids are.
Hoenn: Probably a tie between TensionShipping and ContestQueenShipping at the moment. ContestQueen will always be my forever Hoenn OTP, so they’re going to be a favorite no matter what, but I’ve been having so much fun with Drew and Harley’s family (and their dynamics with Lisia and May’s family) that I feel like they deserve a shoutout as well.
Sinnoh: The BrokenShipping family is a forever favorite just since it’s one of my weirdest ships. It was basically an in-universe crackship to start out and then the more I thought about it the more I thought it would be great. They’re an unconventional family but one I love working on. Shout-out/runner up goes to the ComaShipping family though since how could I not love Paul and Ash and their goth babies.
Unova: I know this is kind of cheating since it’s like five families but… the Montfort family. All of them. I don’t know how it got so big but all of them are so much fun to work with and I’ve just put some of my most effort into worldbuilding Unova that they’re kind of my babies. Even if some are trash babies like Grimsley and Hymnia and Mindy. And while this isn’t set in stone yet… there’s a good chance the family’s going to be expanding once I incorporate Galar 😉
Kalos: PerfectWorldShipping. Hands down. I have… trouble with Kalos, mainly due to lack of inspiration, so I think it’s probably no wonder that the couple/family with a convoluted story and angst and drama is the one I like best. Florian’s one of my older fankids as well and while he’s changed a bit over the years he’s still one I’m very fond of. I really like thinking of him and his dads being soft together.
Alola: Another region I find myself having a bit more trouble with, but I’d say maybe SnowLilyShipping? Mainly just since they start out very typical but end up being very unconventional with their half-alien meme son, sort-of a zombie son, and then adorable baby daughter. Another fun one is the NineIronShipping fam (Guzma/Molayne/Kahili) just since it’s full of shenanigans and all three kids are gremlins.
And then I have some other regions, but those only have one-two families each so I’ll exclude them. Honestly I think it’s just become obvious that the families I tend to enjoy working with are the ones with more drama/unconventional elements. That’s not to say I don’t enjoy the more typical families – I do immensely! It’s just that when it comes down to picking favorites, I tend to go with the ones like that. Really, this AU is more of a personal/self-indulgent project than anything, which is why things get over the top or dark sometimes. I simply want to explore lots of different ideas I find interesting and use this world as a way to do so.