Well, we have the ability to edit 3DS files nowadays, but so far it's been mainly translation and (un)dubbing. It's totally possible, but it would be an incredible undertaking and probably not worth the effort.
It's already possible. There are already 3DS games being translated, and I think I remember something about a hacker putting Ridley's model into Smash. I doubt there's a significant difficulty difference between being able to edit models and being able to edit textures, but I know nothing about that sort of thing, so who knows.
Sure it would be possible!
Someone's helping me to make a unpacker/rebuilder for .arc (darc) files and some other files (like xbb and PAPA in Harvest Moon).
With this, I'm able to rewrite the whole Game (create new events, add npcs, new maps etc).
But right now, I only have Problems with Exporting and reimporting Models (not only for Harvest Moon, possibly will have a Problem with this with Pokemon, too).