I don't follow Skylanders too closely, so I can't comment on that.
I think it's a question of how Nintendo chooses to implement them in the future. The Smash Bros line was fine, cool even. The daily, random items you get with stuff in BoTW or the Warriors games are fine too. If Nintendo continues to implement entire mechanics or modes like certain amiibo in BoTW, Splatoon 2, and Metroid SR though, I think people will start to view them in a less positive light. I certainly feel like I got burned by Metroid SR's implementation, because while I love Metroid, I don't want to have to be constantly refreshing pages to then end up paying a premium because Nintendo decided to not make enough of them. Thanks to that, I feel as though I ended up getting a worse experience overall which... just kinda sucks, man.
I know I'm not alone on that either, Metroid SR definitely lost a few sales because of that. Not enough to make any kind of difference for sure, but if anything could end up causing amiibos to crash and burn, it could eventually be stuff like that.