I see your point, but it's too big a thing to implement, and it can only happen at the end once all the WiaB variables are completed. If SG was developed as a sequel rather than at the same time, it'd be possible, but WiaB needs to be finished, and Season 1 of SG has a completed script. Ocean would have to rework the script to implement the save data, and trigger new renders etc. Will that actually be worth it in 10 years time?
If you avoid Miru, Ayua will still exist no matter what you do. The canon is that Ayua is a Zane, and will be for the next decade until WiaB is finished and saves can be transferred. Would it make sense to you to have a change like that after knowing Ayua is a Zane for that long, having played SG all that time, having seen the whole development of both games already? It'll be ingraind by that point.
Sure Sasha can be Willi's but it's also not a problem if she is. All it means is that Nika is definitely not Willi's if Sasha is. Those are mutually exclusive facts according to the ToS that Ocean abides by. There will never be a problem like that. Ocean won't allow paths to exist that would jeopardise SG, which is his main income. Players will not be able to choose those kinds of paths that would cause problems. You're assuming that OCean will allow choices in WiaB to threaten his source of income. Right now, SG in effect props up WiaB. Simple - in your scenario, Elena and William decide to separate, because Elena gets pregnant to someone else. in the time between the end of Wiab and Sasha's conception, or any variation of things that happen after the player's ending in the year after. Solved.
Also, she is not the only LI that is the daughter of a possible LI in WiaB, we simply don't know what might or might not happen with Daphne, Dana, Mon, Gina, Zoey, Kat... We don't know Elena is a LI right now. Heck other than Miru, we don't know if any of them are