I think what they should do with Y'shtola is obvious:

-find a way to cross dimensions
-return to the First
-it turns out Runar got a girlfriend in the mean time
-Y'shtola realizes that she might actually either a) have had feelings for Runar all along or b) have a part that wants to eventually settle down herself and start a family
-she has to decide how she wants to proceed given her ability and perhaps perceived duty to the star
-involve Matoya somehow, maybe Matoya dies of natural causes, cause she's old
-realize that Urianger and her would actually be a match made in heaven

one of the coolest things Final Fantasy does is make boring, bland and one-dimensional characters with superpowers relatable and grounds them in normal human stuff. This is why Terra from FFVI is such a great character, in the second half she really becomes an actual person when she finds something in the world to protect and care about. And it just so happens to be an orphanage full of children who lost their parents in the apocalypse, which is about as normal and grounded as you can go in FF.

It's also obvious that the game needs more romance, there is barely any. You can say that it's because of the player who should be able to you know pretend that they romance any of the cast, but let's be honest that's just fanfiction at the end of the day anyway. Also just because you want to roleplay your char being in love with Y'shtola doesn't mean that Y'shtola has to therefore become some sort of extension of your wish in terms of writing. In FFX I wanted to romance Lulu rather than Yuna, did I get the option? No and it's better that way. You can still flirt with Lulu tho, which is nice! Still she decides for Wakka in the end, cause she's her own person.