I've said it in this thread and I'll say again that I am a huge Nintendo fanboy, and that I agree there's no reason there can't be an eshop equivalent. Just wanted to preface this post with that info.
In the end, the real shame is that all of this is attached to a brand new 2D Metroid game. This isn't the first time Nintendo has done this, and I can see how people would be upset about it like I've said, but I wish this anger and talks of boycotting had been applied to the Twilight Princess remake, or Captain Toad where I think you got extra levels? Don't quote me on that.
I find this happens a lot, in all mediums. It just happened yesterday to a Broadway show that in my opinion was probably the most innovative show in a long time. Great Comet just announced their show is ending after about a year, because of a controversy with one of their leads. Of course whitewashing is a large issue in TV, Hollywood, etc, but in this case they had a black actor in a role, and decided that after a month or so of him being in that role that they'd replace him with Manny Patenkin (sp?) to help sell tickets. Keep in mind this is already a majorly diverse show, but people took their anger out on this show and ultimately torpedoed ticket sales, ending its run.
I feel the same thing is happening here, just with a problem that is probably much less serious. It feels like people have randomly decided to vent their amiibo hatred on a new Metroid game of all things. It remains to be seen if this thread is a vocal minority, or if it reflects the views of many 3DS owners, but I will be so bummed if all this talk of boycotting succeeds and ends with Nintendo taking it the wrong way (you know they would) and meaning we'll have to wait another 15 years or whatever for them to touch what is one of my favorite franchises ever. Sorry for the long post, I'm just so excited for this game and want to see more of this franchise
tl;dr: I wish that as fans of video games we had chosen to protest this amiibo business when it started, rather than on the release of what feels like a unicorn sighting