I don't understand. Why do you need something to backup your game cartridge?
I was goofing around with my save file - you know, the thing that's stored in the memory card of your 3DS? It's all there, from what I can tell.
The file is 1024 KB in size, though if you hunt through your 3DS's memory card it may take a little bit to find - it's not labeled or anything. You can tell it's your save file because deleting it deletes your data and trying to manipulate it in any way causes the game to say your save file has been corrupted upon starting Pokemon.
Like previous pokemon games, the savegame file has a checksum. The data here is also encrypted in some way, trying to search your save file for your money value, name value, playtime, etc. is pretty much impossible, as it's stored differently than how it's retrieved. Plus, there's that pesky checksum. Trying to change random values on your save without first knowing how to alter the checksum isn't going to work either.
I'm not an expert on how pokemon save files are constructed, or anything, but I thought I could be a bit of help. I wrote a simple java program that compares two save files and prints out a textfile of lines that don't match up. Using this approach, you can begin to identify where the checksum is stored and how it's effected, as well as how various data is 'encrypted'.
I've already done an analysis of my own save game, the two saves I've included in the below zip are about 1-3 seconds apart, the only difference between them is the playtime (I may have moved a few steps as well, I forget). It's open source, so you can verify the java code contains nothing malicious. It's a very simple, very basic program you run from the command line.
If anyone is interested in playing around with their save file, you could probably figure out how to hack your money, inventory, playtime, and other simple data, if you put enough effort into identifying what changes and how - previous generations only 'encrypted' data by XORing the hex values. Editing entire pokemon is probably not going to be around for a while, but you can at least make your life easier, I know I have no desire to farm hundreds of those 'change pokemon ability' items. But, I'm not sure how to go about cracking the checksum. I'm sure there's someone with more expertise who can do that quicker than I.
I haven't tested this program on any machine but my own, but it should work fine. It's just supposed to be a tool of convenience should anyone want to inspect what's going on here.