My stance is, okay, you bought the Amiibo. It's ~$15 or whatever. Sure, it's more expensive than many types of DLC. But unlike most DLC, it can be scanned into a wide variety of games for various effects. Some are minor, some are a bit more substantial. But it's definitely more than just a one-off.
The Metroid Amiibo will surely have an effect in Prime 4 and more. So pretty sure this won't be the only use. If you're a fan of Metroid, odds are you already have the Smash Metroid Amiibo, and likely want the new ones, too.
Basically, I see no problem with this. I have all the Zelda series Amiibo as well, and while an expense, I'm sure they will continue to have uses beyond BotW.