You will use the 3DS System Transfer from the System Settings -> Other Settings menu (sub selection/page 4).

The menu options should be the same on the New 3DS even if they're shuffled around.

The process will transfer everything over from the old 3DS to the new New 3DS except for anything that was a part of a pre-installed bundle (eg, if you bought a 3DS with Mario World pre-installed, that will not transfer over).

When the process is done, the old 3DS will be reset to it's original state as when you originally bought it. Note, that most DSi Ware save game data and some DLC (no list on hand but it can be re-downloaded) may not transfer in this process.

You will loose DSi Ware save game data and will have to replay those games to unlock stages etc. (some examples of this are Mario vs. Donkey Kong Minis March Again and Aura-Aura Climber).

I just recently did some 3DS system transfers of DSi -> 3DS and 3DS -> 3DS recently and talked to a Nintendo support rep to confirm some steps in the process and also talked about future New 3DS migration and I was confirmed that once the hardware is out in the region they will update the relevant support pages with any changes, so check there first before you do anything and when in doubt, call their support line.

NOTE: Relevant info from the Nintendo Support site. 1) do not setup your NNID on the new system before the transfer process. 2) If the SD card you have on your old system is a standard SD card that is greater than 4GB, you will need to buy a Micro SD card (with an SD card adapter) and using a PC, copy the contents of that SD card to the Micro SD card.

Only the New Nintendo 3DS has swappable faceplates. The New Nintendo 3DS XL does NOT have that option.

Sources:

• Destructoid:

  It's a common sentiment, I'm sure, but I'll say it anyway: too bad the New 3DS XL doesn't support swappable face plates. As much as I like the designs, if and when I upgrade, I want the big screen.

• Crave online:

  The problem is that North America will only get one New 3DS option, and it’s the New 3DS XL. The New 3DS XL doesn’t support faceplate swapping, so consumers will be stuck with only two color options at launch, neither of which stand out nearly as much as their New 3DS counterparts.