It's interesting that you bring up Nintendo of America. From what I understand, the reason Nintendo seems the most aggressively protective of their copyrights out of the big three game companies is because unlike the other two, their headquarters is in Japan, which has different copyright laws than America. In certain areas - particularly parodies and spin-off works, the latter of which Uranium technically falls into - they're stricter than ours.
That said, since the DCMA didn't come directly from Nintendo - from any country at all - or TPCi, I will agree with you that it is a case of lawyers trying to please their retainers by doing something before they're told to.
I will also agree with you that the best thing we can do in this situation, in terms of protesting, is pass Uranium basically from hand to hand, let it saturate the internet, and let it not die. When Sun & Moon come out, and the day-one sales are higher than ever, let it send the message that fangames do not hurt the official games, but in fact help them retain the hype for longer.
(it should be noted that when I was much younger, I was adamantly against fanmade games. But I feel like in the past few years, the quality of fanmade spin-offs has gotten better and better. Newer Super Mario Bros. Wii, Pokemon Insurgence, Uranium, etc. The technology has gotten to the point where if you have an idea you can make it happen even if you're not a professional. Does that mean that professional game designers are obsolete? No. It just means we're closing the gap rapidly.)