Ok kids, listen up: nobody "won", this ain't a dick length contest. Nobody here is either a Nintendo hater or fantard. Sometimes, reality is way more complex (woa, amazing)
Nintendo formally told the developers to not use their IP, since by being the rightful owners of the Mario franchise, they are legally able to enforce actions aimed at keeping the integrity and image of their brand the way they like until it enters the public domain. This kind of action is usually known as a DMCA notice.
Every single person at the game development side of nintendo is always flatered and amazed by fan proyects, but one thing doesn't nulify the other. The problem here is that things like the Mario Brothers franchise have become such the pop culture icon that many people forget it's someone's property, and proceed to call company A or B assholes.
The sheer ammount of love that our little jumpy plumber gets makes it resourcewise imposible to closely monitor every single fangame, modding project, T-shirt maker etc...The inevitable solution is to be this strict, since being selective and allowing a handful of things and disallowing others is both unfair and illegal.
Precisely, comparing recent SEGA's apparently more permissive stances on this matter shines more light onto this. The volume of fan-things SEGA has to monitor is actually posible to manage, and more curated due to it's relative smaller size. (That, and the fact SEGA needs all the love they can get these days). It's not a matter of "company A gets it and company B does not and are a bunch of pricks" It's a boring, surprisingly straight forward problem of logistics
The devs obliged and changed a bunch of visual and musical things to keep the game's core concept intact while avoiding further conflicts of interests. End of story. Sorry, no evil companies and martyr developers here, only legal stuff.