I'd love to incorporate Snow and Yukine in some way. Since he's, well, Japanese, it'd be a little awkward to AU it that he's Snow's bio kid (like Stiles & Emma are now actual siblings in this AU) so maybe incorporating Yukine into that could work? Emma and Stiles are both hunters so it'd make sense that Snow's third kiddo would want to follow in those footsteps?
Alternately, since we're going for the approach that Snow gets separated from Emma and Stiles once she's turned, maybe she meets and bonds with Yukine after she's turned and kind of adopts him from there? Maybe he knows she's a vampire, maybe he doesn't - but Snow was a hunter before she turned, so she could at least teach him some basic survival aspects.
If you want to do something different from usual game canon and go a different route with an AU Yukine, I could offer any of my other hunters for him to interact with (Arthur, Athos, or Bull).
For everyone else, I'm all for doing body memory things for Porthos and Freya - have it be that they ~meet~ for the first time in this AU and have a connection? Or have them already established as knowing each other.
I find it kind of amusing that out of the four musketeers, Porthos is the only vampire lol. Awkwardly friends with two hunters and then the perverted priest. By which I mean, obviously we'll need some Porthos & puppy shenanigans. Although I'm sure that goes without saying, considering.