I doubt they will move away from the owl statues, but they certainly could add more to make saving the game much less of a hassle. For instance I would add owl statues at the Pirate's Fortress, Ikana Graveyard, and Goron Village at least, but really I don't see how it would be a bother to put them all over the place. For instance there are already two in the swamp, but it wouldn't hurt to have statues by Kotake's shop, the swamp spider house, and the swamp shooting gallery. As DarkestLink alluded to (edit: and Ganonking) there isn't any reason to not add more flexibility in moving forward through time. I think the Song of Double Time should enable the player to set whenever in the future they want to go to just like the wait feature in Elder Scrolls games. Those are the two most bothersome things about the game for me.
There's also huge room for improvement with all the masks that had somewhat meaningless existences beyond gettting a heart piece or two. For instance they could make the All Night Mask reduce damage taken (or increase damage dealt) during nighttime hours, make the Postman's Hat slow down the clock during minigames (as an allusion to his timing practice and making the shooting galleries easier to beat which is something I've heard people say they couldn't do), make the Couple's Mask lead to female enemies refusing to fight you (think Pirate's Fortress), and let the Keaton Mask increase the likelihood of rupees appearing from grass or pots (since Keaton shows up at moving groves of shrubs that always have rupees). The possibilities are endless.
I'd also love a master quest. I brainstormed ideas to make the dungeons harder in the past. Something the game's dungeons didn't do was take advantage of the cyclical nature of time. For instance you could force people to complete dungeons across two cycles by having only one key for two doors. I could imagine people being stuck on that for a while since it's generally safe to assume that a dungeon can be completed in a single run. This game is my favorite in the series, but the ways Nintendo could improve upon it are tremendous imo.