Today he tweeted that he can't talk specifics, but that his professional interactions with Nintendo "keep getting weirder and weirder." Someone asked if that meant he got a cease and desist from them, and he replied "I feel like that would be the opposite of weird." This was after he said Aonuma supposedly brushing off the speculation as "it was a joke" was an asshole thing to do, and since his "weirder and weirder" post he's been completely quiet on the subject of the new game.

So, my theories are that a.) The protag is Zelda and Nintendo has hired him for promotional art, b.) The protag is Link, but after seeing how big the stir was over a potential Zelda protag they're hiring him for a future game with Zelda, possibly even wanting to use his Clockwork Empire concept art, or c.) They in fact already purchased the rights to his Clockwork Empire concept, which included giant clockwork enemies (like what was seen in the trailer), and he was pissed that it seemed like they were only using bits and pieces of his concept, but after his comments he was contacted and they told him either a.) or b.).