I do support Operation Moonfall, but I think Axel (who is against it) did make a good point in one of his videos concerning the topic when he said that if it was released now it would be lost among all the other Zelda material Nintendo is pouring down on us, just as it was lost among Ocarina of Time, the Oracle games, and The Wind Waker at the time of its release. I do want to play a 3DS version of Majora's Mask at some point, but I can agree that it might be wise to wait a little bit in order to make sure it actually gets noticed, and Zelda's 25th Anniversary isn't necessarily the best time to make it stand out.
I think we should consider, though, that Majora's Mask was released originally at the end of the Nintendo 64's life, with the GameCube already announced and the PlayStation 2 already released (granted, the latter's outside of the realm of Zelda). With a 3DS version of Majora's Mask, however, they'd be releasing it on an entirely new console that frankly doesn't have very many games for it at this point. Right now, almost anything released for it, particularly any brand Zelda, is going to get noticed.
The way I see it, 2012 should be a good year for Majora's Mask 3D. Considering how long it takes to make good console games, I would be surprised if the Wii U Zelda title was completed before 2013. Perhaps a 3DS Zelda title could be released during 2012, more likely so if they've already gotten started on it, in which case they should distance it from Majora's Mask 3D as much as they reasonably can. Release Majora's Mask 3D earlier in the year, perhaps shortly before summer (which they can surely get done, especially if they employ Grezzo again) and the original 3DS title closer to Christmas. Skyward Sword would already have been out for a number of months with a number of months left for a 3DS Zelda title (if that comes forth at all), effectively isolating Majora's Mask 3D's release so people actually notice it.
And people need to notice this game. It's my favorite Zelda game so far (effectively making it my favorite video game overall), so I'd love to see it get the recognition it deserves.