Nintendo has already stated they don't listen to petitions, also boycotting Metroid II on the eShop won't help either.
Really, there's no reason to get up in arms. Nintendo's in their rights. Sad, but true. Yes, there's a case to be made to fight for fair use and deriative works. No, it's probably not worth it in Doc's perspective.
We have the game. It's complete. Go play it, continue to share it. No more patches is sad, but it doesn't mean that what we have is suddenly gone. AM2R is here. It's a fantastic, COMPLETED game, it's in the wild. It released, it's nothing but a success story, to EVERYONE involved.
So just, put down the pitchforks, guys. There's nothing to fight for. We already WON.
And Milky here is right. The game was infringing and Nintendo's actually been really nice about it to not send a C&D or DMCA when AM2R was in development. I remember years ago, there was a Zelda fan game being built (I was on the forums of such), and the creator got a C&D when he was barely in the starting stages. He was still building the engine and a lot of his screenshots were mock-ups.
Though, Milky, where did Doc say there would be no more updates? I'm sure I heard there was an update coming soon with a buffed Serris and bug fixes?
Edit: Just saw Doc's Tweet. That's very sad.