I say that amiibos would be the absolute best option for exclusive content, because its the only type of exclusive content that you don't need to own the hardware for in order to own and enjoy.
We do already have amiibo for other third party characters. Sonic, Mega man, and Pac-man, so clearly there is already some sort of licensing format worked out for amiibo sales and third parties. We don't however have any third party games yet which feature amiibo, so maybe it wouldn't work out, or maybe no third parties have earnestly pursued it. Regardless I still think it would be a great idea.
The one legitimate argument I see against it is exclusive amiibo locked content within the game. But this content is not expected by anybody to be substantial, and nobody will be disappointed if it is not. There are some examples of some games perhaps overreaching on how much content to lock behind amiibos, but the thing to remember is that this content is a decision for the developers. Playtonic would be able to provide amiibo locked content that nobody would have to feel sorry for missing out on on other platforms.
If Yooka-laylee were to get amiibo support on Wii U, we could all be able to get something really cool out of it, regardless of which platform we purchased the game on.