It is safe to say that Ruby and Sapphire remakes were going to eventually happen. What Nintendo did was great as I am positive that they were probably evening developing the game alongside X and Y and decided only to focus on X and Y and decided to announce OR/AS when XY was starting to get a bit stale. Good job Nintendo! :clap:
As others stated before me, Nintendo doesn't really develop the Pokemon games but instead GameFreak. As much as Pokemon is very related to Nintendo, they don't really develop the Pokemon games, so when the subject of Omega Ruby and Alpha Sapphire hindering the chances that we will get a Majora's Mask remake, I highly doubt it would. For all we know, Nintendo might be even working on the project right now and are simply keeping it discrete from the public and might reveal it until the timing is just right. However as much as many people love Majora's Mask, the fanbase for such a remake is very minuscule compared to the fanbase of Ocarina of Time. Ocarina of Time was huge and considered the greatest game of all time until Super Mario Galaxy took its place. As much as the Operation: Moonfall was huge, it still falls short of how many people actually care for the game. At the end of Operation: Moonfall, the Facebook page had over 90,000 supporters and that is phenomenal, but then you look at other Facebook pages such as Zelda Dungeon and Zelda Informer with over 300,000+ and 200,000+ respectively and you can clearly see the huge difference in support.
Now when it comes to the possibility of a Majora's Mask remake, I firmly believe that it is in fact quite possible. Nintendo has the proper coding, funding, and will probably have their 3rd party company GREZZO help out create the remake. So why hasn't this happened already? The problem is that Nintendo is suffering from their third consecutive loss in profits and while a lot of people are still interested and will probably buy Majora's Mask 3D, it is really a huge risk. There's no denying that the fan base of Majora's Mask is just minuscule and I'm sure they don't want to take the risk of losing money even though there are still a vast amount of people waiting for such a game to be released. Maybe if Nintendo wasn't having financial problems we could have easily seen an announcement for Majora's Mask 3D right now. Do I still want a Majora's Mask remake? Yes. Will the game sell? Perhaps not enough to Nintendo's expectations and that's where we find the connection, because Nintendo does in fact listen to the fans, they do want to please us with their games but it is because the lack of support is why Nintendo is still holding back a remake of Majora's Mask.