I don't think Amiibo have gone too far, yet. I can understand concerns that they might, but at the moment i think Nintendo have got the balance right.
As of yet, I haven't felt I have missed out on anything by not owning any amiibo other than the Donkey Kong one. Mainly the features are cosmetic and don't really affect the game in any meaningful way. I had a look at the Donkey Kong compatibility list, and i can use him in 10 games. Which is good value for money.
But more importantly, i feel i'm not missing out because 99.9% of games are feature packed as they are ( except Smash Tennis). Hyrule Warriors and Smash for example have enough content to justify several games worth of content. Adventure mode in Hyrule Warriors for example could have easily been sold as DLC. So in that sense i feel i am getting a fair deal. I don't feel shortchanged by it. They are just optional extras on top of a whole lot more.
Even in Mario Kart, The DLC for 16 new tracks was only £11. Extremely good value for money and in Mario Maker you can actually unlock all the Amiibo stuff in game.
And in Splatoon we got free content for 9 months or so, of course some of that should have been in the original game, but i feel Nintendo have added extra on top of that as well.
Also the pricing of games comes into account here as well. Most Wii U games of late have been released with a price mark of around £30. Captain Toad and Splatoon were sub 30. So all in all i think , for myself, the value of what they release is pretty much spot on.
I understand concerns though, they are only one game from pushing the concept too much and then more people might turn against them. Whether they can maintain that balance of being acceptable is hard to gauge, especially as more and more games use it. I also feel that they should offer some of the Amiibo functionality as proper DLC for users to buy as well such as the Splatoon map remixes or even better do it like Mario Maker and have the ability to unlock the content, but not all of it, having a replenish your health once a day for say £2.99 is a micro transaction in all its nasty form.