The New 3DS XL System Transfer process is a bit of a mess due to the fact that the New 3DS accepts MicroSD cards. Even if you're only shooting a few licenses or a couple of games across to your new handheld, it's fiddly and annoying, but nowhere near the levels of hassle you'll encounter if you have Gigabytes worth of data to transfer over!
We're a bit late to the party, but just in case you've yet to take the plunge, I'd like to offer you a way of cutting down on a lot of hassle by essentially future-proofing your New 3DS before the transfer ever even takes place, granting you all the storage you'll need and a much easier transfer to boot.
For the record, here's the traditional PC transfer process in full (which you can avoid if you've only got a few files to transfer by using the Wi-Fi option, though it admittedly takes 2 hours per Gigabyte!).
- Go through the setup on your New 3DS, download the latest software, but do not create a new Nintendo Network ID on this system as it will overwrite your old one.
- On the home menu, go to System Settings, then Other Settings, then System Transfer.
- On both systems select "Transfer From a System in the Nintendo 3DS Family." Select "send" from the old system and "receive" to the new one.
- Follow the prompts to confirm the transfer.
- Select "delete" to erase the content on the New 3DS's microSD card.
- Select "no" on the New 3DS to confirm that no other microSD cards have been used with the system.
- Select "yes" on the old 3DS to confirm that you're using an SD card (these come with the system, so you likely are).
- Select "PC-based transfer."
- Select "move" on the source system.
- Once this is complete the old 3DS will format and the New 3DS will restart.
- Power off both systems and remove their SD/microSD cards. This will require using a size zero Phillips screwdriver to remove the back panel on the New 3DS.
- Connect the SD card to your computer and copy the folder called Nintendo 3DS to your desktop.
- Connect the New 3DS's microSD card to your computer and copy the folder from step 12 into it.
- Insert the microSD card into your New 3DS, reattach the back panel and power the system on.
There's a better method, though, that I personally used last week and haven't seen around much. You'll need all the kit above, along with a new MicroSD card with plenty of storage (preferably 32GB unless you correctly format a higher capacity card, and don't scrimp on the read/write speed, since it does affect loading and menu population times) and MicroSD -> SD adaptor (which are usually included with MicroSD cards these days).
In effect, we do the fiddly bit first. Just pop your SD Card out of your old 3DS, copy all content across to a folder on your PC, then copy it onto your new MicroSD card. Easy peasy - you can do this bit at your own pace. Once done, then put the MicroSD card into its adaptor and put that into your old 3DS. Whereupon it should function exactly like before - test and make sure.
Then follow steps 1-6 above... until you get to step 7.
See, you're not using an SD Card any more. You're using a MicroSD card in an adaptor. So select 'no,' at which point a simple license transfer will occur.
Once complete, do step 11, then remove the adaptor from your old 3DS, remove the new MicroSD and put it in your New 3DS. Pop the screws back in and you're done.
The benefits are twofold. First of all, you'll sorted out the fiddly PC file transfers at your own pace without having to touch a screwdriver or move any backplates, while also making sure that any pre-installed content licenses on your New 3DS are transferred to your account correctly (such as the Monster Hunter 4 Ultimate Edition). More to the point, though, you've also just future-proofed your new console with all the storage space you need and won't have to open it back up again down the line.