I'm not one of the people working on it so I could be wrong, but from my understanding the problem is getting past the 3DS's encryption methods to put the edited save file back on the game cart. Since its not something that we know how to do, you can't really make an estimation on it. A breakthrough could happen tomorrow and we could be injecting Pokemon next week, or it could be months from now when that breakthrough happens. People are activly working on it and it most likely will be possible sometime in the future, but no one knows exactly when.
EDIT: The problem is reencrypting the file because we can't get it past the AES-MAC yet, not the 3DS's encryption.