Please get rid of the boats. Give Link a Dolphin so we can just Wave Race our way around the seas. Transitions between modes of travel should be seamless.
Anyone else remember the rumors that the horse in TP was really a shape shifter named Poseidon that was also the hawk and wolf? I loved that idea (even though I doubted it was true back then), and I'd love to see it done in a future Zelda game. Link apparently has to have a talkative companion, so it might as well be some sort of little whatsit that can both hide in his pocket stating the obvious and do useful stuff. It would even make a good excuse for lengthy overworld quests for new animal forms, such as a creature to ride across the sea.
Regarding a non-Link character, I just don't see that working from a story perspective, or at least not the way I see it. It's not simply always Link, but rather it's always the Triforce of Courage. The following is based on my own inferences from the games, and future developments could shoot it all down, but it's how I view the Legend of Zelda series.
The Triforce of Power made Ganondorf into an immortal evil godlike being in response to his desires, but the Courage and Wisdom counterparts responded to Link's and Zelda's desires to stop him. Since Ganon is immortal, Link and Zelda are reincarnated by the Triforce whenever he is close to regaining enough power to be a threat again. Zelda always reappears in the royal family because Wisdom dictates that that's the best place to be to get ready to fight Ganon. Link, however, always ends up someplace more "fun" due to the influence of the Triforce of Courage. It protects him, but by nature it pretty much has to put him somewhere where he'll have great challenges to overcome, or at least where he can get regular adrenaline rushes.
Now, since it's the Triforce of Courage's response to the original Link's wish to stop Ganondorf that drives the legend, it simply does not make sense for some other character to be the hero, or even do some of the work for him.
That's not to say you can't do more with the series than the usual Ganon storyline, as my favorite entries prove. For one thing, Nintendo could explore why the Master Sword already existed before Ganon appeared (if Ocarina of Time explained anything, I've forgotten it). It would even be harder to include Link in such a game than not.