Remember back in 2013 when this happened?
http://www.polygon.com/2013/7/9/4508826/super-smash-bros-melee-pulled-from-evo-livestream-nintendo It was Nintendo of America stepping in and doing something kind of ridiculous which really pissed off the fans of their game and had provided the company with no benefit whatsoever. This was brought to an end when Nintendo of Japan became aware of the situation and told Nintendo of America to chill out.
I talked to someone at Nintendo of America yesterday who said that the best thing we can do is contact Nintendo of Japan and tell them about the situation. Explain to them that this is something the fans want and that it is not in any way preventing them from selling official games, in fact it is promoting them. I was also told that the notice on record for when the AM2R was taken down - which we were unable to confirm as being the AM2R takedown request, was of the type commonly issued to rom websites. AM2R could have been confused for the rom of an official game.
TLDR; If you want AM2R back up, contact Nintendo of Japan and politely explain the situation to them.Calling Nintendo of America could help as well.
Nintendo of Japan contact info: 011 81 75 662-9600 [Need Nintendo of Japan Email!] Fax: 181756629620 (country = JAPAN)
http://www.sendfaxinternet.com/;
Nintendo of America contact info: 1 (800) 255-3700
https://www.nintendo.com/corp/webform.jsp