No, we can backup and replace save files, but Nintendo has them encrypted and checksummed (as I recall). Editing save files would be a major progression point for hacking the 3DS, if the Twilight Hack is any example.
As others have said, no. The best you can do right now is use other peoples saves for pre Mario games using the save dongle. Anything else causes the save file to be erased.
No, there's no way to hack anything related to the 3DS, except for DS mode via the regular DS flash carts (and of course, this does NOT include 3DS games).