I just imagined something that has not yet been implemented in the Zelda series (in terms of storyline, and perhaps in gameplay) and I guess it could be a plausible next step:
You take control of two different links in different periods of time, each with an unique storyline at the beginning and maybe they could find a portal in which they could get to each other's era, merging each other's storyline and there you go, two links joining forces to save Hyrule in two different periods of time. I think it could be interesting. Maybe find a link between the 3DS Zelda and the Wii U Zelda... Maybe it's a lot like Four Swords/Four Swords Adventures but hey it's worth the thinking.
You take control of two different links in different periods of time, each with an unique storyline at the beginning and maybe they could find a portal in which they could get to each other's era, merging each other's storyline and there you go, two links joining forces to save Hyrule in two different periods of time. I think it could be interesting. Maybe find a link between the 3DS Zelda and the Wii U Zelda... Maybe it's a lot like Four Swords/Four Swords Adventures but hey it's worth the thinking.