I made a post a while back where I took 10 (maybe 15, not sure) unlikely things that could happen in the future, and had people state their opinions of them. One of them happened to be if the third Oracle game (MSoC) were to be released somehow on the 3DS. Personally, I don't think it will happen, and if they did, I'm not sure how they would be able to integrate it into the oracle games' linking feature, unless they re-released the others. As awesome as that would be, it just doesn't seem likely that Nintendo will ever do this. A few reasons being:
1. There would be confusion for some players who would buy the Oracle of Seasons and Oracle of Ages games, and attempt to link them, just like they did with the original Gameboy releases. These players would attempt to link them, possibly not knowing that they need to deal out even more cash a third game that they didn't know existed.
2. The game is probably not complete, and I doubt Nintendo would be able to get Capcom in on the recreation of the game (considering that Capcom was responsible for the development of all of the oracle games, released or not). Even if Nintendo manned the recreation process alone, there would still be issues. Nintendo would probably not want to release it under the same name, but release it as it's own title and not as the third game in a trilogy. If they did, they would have to re-make/port the old games onto the 3DS but with more unlockable content. Knowing Nintendo's habit of not remaking games, this is unlikely to happen. (We're lucky to have OoT on the 3DS. We really are.)
So, in conclusion, I would like to see this happen, but it probably won't. Sorry. Unless someone else wants to prove me wrong.