It's their IP plus Nintendo knows that AM2R is better at least for fans, I didn't play federation force but AM2R is more appealing to me. The developer of the AM2R has enough talent to develop their own 2d metroidvania, at least technically, they just need to use their imagination.

Nintendo has always been the harshest with taking down fan made content, even freaking movies. Personally, I agree with what one Youtuber said, Nintendo should make a portal to put all of these movies and games in. They can approve them, of course, just so it keeps with their family friendly approach. But, just put up some advertising and give a percentage of it to the creators of the content. Problem solved.

Honestly, why even bother? It's on the Internet, it'll stay there as long as people with the game have an Internet connection, nobody gains anything from this except from truly, truly sad people. Maybe they're using this as a escape goat to blame for Federation Force's failure, and keep themselves from waking up from thee fantasy world they're living in, wouldn't put it past them really.

This specific website I believe had ad revenue generated and had revenue sharing with the uploaders. I think Nintendo and other companies are aware it is the "Internet" when they do DMCA, but they have to protect the trademark etc. 

So if I put the file in my mediafire account to share this game to others will I get a cease and desist order as well?

The whole issue of "fair use" really needs to be looked at, but while lawmakers are being pursued by lobbyists, it will never happen.