Well not everyone is interested in the figures and there's no other way to get the content. So from some people's point of view it is just $12.99 DLC. If they added the option to just the content separately for like $1 or so I think there'd be a lot less complaining.
If they did that, then there'd be no point in the amiibo.
Maybe if amiibo didn't exist they would do it that way, or we'd have an in game challenge mode, or the content was created as an excuse to have the amiibo as Nintendo is pushing this IP hard. It's hard to say, but if down the road those amiibo get made compatible with Smash, or Mario Kart, or some other IP they might have more "value", but right now they stand at 20 bonus, non story/main game missions plus rewards for 13 bucks per amiibo, so 60 missions for 39 bucks - Not entirely horrible given some other company's practises. Look at Batman Arkham Knight with it's 40 dollar season pass which does include story missions, or how Catwoman was locked out of Arkham City unless you pre-ordered.
People have been screaming at Nintendo for years to "get with the times". This is how they've chosen to go about it.
Catch 22, can't win or lose regardless of what they do. Whether it works out long term is the gamble.