No, because I didn't say it's fair-use. I said there is no precedent, where this happened or was argued in front of a court; hence the legal situation is not as clear-cut as you make it out to be.
To sum it up:
-> AM2R is most certainly trademark infringing, because it carries Metroid in its name.
-> AM2R is most certainly a derivative work, because it is based on Metroid 2, so it is copyright infringing.
It would still be legal, if it falls under fair-use. Your point: It does not. My point: It might or it might not.
So let's review the complete fair use factors (not copy and pasted):
https://en.wikipedia.org/wiki/Fair_use#U.S._fair_use_factors
1.) Purpose and character of the use
[+] AM2R is transformative and non-commercial
2.) Nature of the copyrighted work
[-] AM2R is fictional.
3.) Amount and substantiality
[+] (To my knowledge) no art assets whatsoever, no data, no files directly from Nintendo were used. Everything was redone. Substantial amounts of content differ between original and remake. Designs are similar, just like fanart designs, which definitely constitute fair-use.
4.) Effect upon work's value
[+/-] AM2R has a very positive effect on the trademark Metroid and increases its value, as it keeps the name Metroid in media, when Nintendo more or less abandoned it. It will not have a negative effect on Metroid 2 GB sales (+), but you can argue that it is a direct substitute for the original work (-).
So yes, you can argue both ways. And that is entirely my point: It is not clear cut.