To be fair, they shut it down because if they didn't, it would appear that they were not protecting their copyright and would therefore lose it to public domain early. Seeing as how they ARE doing stuff with it (such as the re-release with extra content and a bonus ending to tie it into Chrono Cross), I believe they may be planning to continue that story someday soon.
As for this Metroid 2 remake... as long as it does not contain plot elements from the original version (as in, text and such) it may fall into the same territory as the Super Mario Kaizo World games: fair use.