It'll certainly do more than going along with it. This is the first time they're showing and telling you that they have no problem locking standard features behind Amiibo DLC. It's not going to change unless people make it clear to them that they don't want this shit in their games. People may their voices clear enough with on disc DLC as well as season passes last gen and they eventually went away. As of now with Amiibo DLC we've had people either pretending it wasn't DLC or just making excuses for it because at the time it was small content and not anything that someone would consider substantial. But that's all led to this. Now it's a difficulty mode. For the next Smash it may be an entire character.
I'd agree if this were Mario Odyssey or Splatoon 2 people were boycotting. Metroid has a history of not selling well, so if another game doesn't sell well Nintendo isn't going to see it as enough of an anomaly to take a step back and look at things. They'll just see it as another case of Metroid not selling well and, instead of evaluating their position on Amiibo, they'll evaluate whether Metroid is a worthwhile series to pump money into in the now-fully-HD future.
Already done all three. Nothing will change unless it hurts Nintendo's bottom line, and I'm telling them why I'm hurting their bottom line so they make damn sure they know.
I highly doubt the head team at Nintendo of Japan will ever notice one guy making a few tweets at the Nintendo of America months before Samus Returns' release date. All they'll notice is the sales figures at the end of the Fiscal Year.