[marlz]

Depends. While I think the idea would be pretty nifty, MO was built to specifically work with the 3D environment, so it would be an interesting and rather difficult challenge to adapt it backwards 1/2 to a whole dimension.
It would probably end up being the biggest reimagining of the remakes (starting off with New 'n' Tasty), especially if they wanted to add back in all of the content that never made it in to begin with... Mudokon Queen, plotplotplot!
Then there's the matter of the rest of the Quintology. Three more games at least to follow up MO, and do keep in mind that plot carries on from one entry to the next so anything planned for MO may possibly be in the next entry instead, provided the game is long enough to accommodate the story.
And of course, the fact that they're giving the HD to MO as it is. Would they bother to do so if they were thinking of just retconning the whole game and starting it up again from scratch? Sure, New 'n' Tasty is a reimagining of AO, but the original game is still essentially there, so I have a feeling this neostalgic rebooting will only be given to the first two games at most.

That being said, I do still love the idea. It would be interesting to see the game working like that instead of in 3D, and from what we've seen of NnT the perspective and scrolling could make some MO ideas work well in the new format, I just don't think the plot and mechanics were built in such a way they can be transferred to a 2.5D environment that well.