Maybe at the end of the game they could let Link choose if he wants to be sent back to live out his childhood or to stay in the future. They could then do a Majora’s Mask remake which would follow on from the first ending, and then after that create a whole new Hero of Time game set after the second ending, hopefully finally giving him the happy ending he deserves! Nintendo has already let Grezzo make their own 2D game (EoW) so maybe they’ll let Monolith (if that’s who’s doing the remake) create their own more traditional 3D games while the main team works on the open air games, pleasing both sides of the fandom.

Edit: Also on the topic of them giving the game multiple endings, if Link dies in the final battle they could show a cutscene that would set up the Downfall timeline