I love Nintendo but I do have issues with the company at times. However them taking down fanmade games is the least of their problems.
Its just purely logical, if they let people freely adjust their old games then what sort of precedent does that set? not to mention Nintendo still sells their old games on the E-Shop. Since they don't put their games on any platform except their own, they certainly aren't going to be okay with somebody giving out a free version of Metroid II online that has 1 million downloads and will make it unnecessary for loads of people to buy the title on the Eshop.
There are bigger issues with Nintendo at present in terms of how they operate and work with fans. I would say the biggest is their attitude towards social media and Youtube, the concept that no one can post content that includes footage from their newer games unless they opt into the Nintendo revenue sharing plan. In the big scheme of things that sort of thing just absolutely damages Nintendo's IPs being spread further in social media.
I mean obviously most people are aware of Mario and Zelda and Pokemon but it doesn't do them in any favors when they bizarrely limit when Nintendo game footage (at least stuff from current gens) can be posted online
