Do the new Nintendo 3DS and new Nintendo 3DS XL have swappable faceplates

So... here are some long and shorts to your question.

1) You can chose to not delete some data on the receiving (new in your case) 3DS but only the data on your SD card. See here:

Target System

Tap "Delete" to confirm deletion of all Nintendo 3DS data on the target system's SD Card. Tap the blue "Delete" button to begin the transfer.

If "Do Not Delete" is selected, the Target system will request to perform the transfer without deleting the Nintendo 3DS data on the SD Card. Tap "Yes" to begin the transfer.

No matter which option is selected, you will need to redownload any preinstalled titles on the target system once the transfer has been completed.

When the transfer is complete, tap "OK" to restart the system.

2) Any titles on your system with your Nintendo ID (the old system in your case) can be redownloaded if they're deleted, so long as you don't delete said Nintendo ID. See here:

If you deleted the eShop account of whatever user bought the games, then as far as I know access to the games goes as well. For example, if you have User1 and User2 Nintendo Network IDs on the system, purchase a game under User2, then delete User2's account, you may lose access to all the games User2 purchased. Aside from you deleting the account somehow or someone with access to your system deleting it, I don't know how you could lose access to the games.

3) You can't transfer from old to new if the new system has an NNN associated with it. See here and also in the first link I provided:

You cannot perform a system transfer if the target system has a Nintendo Network ID linked. You must format the target system to remove the Nintendo Network ID link prior to transferring content.

4) Any programs installed on a system without a Nintendo ID will be retained when a Nintendo ID is added. See here:

What is retained:

All game licenses purchased prior to linking a Nintendo Network ID.

Funds added prior to linking a Nintendo Network ID. (See "What is NOT retained" for restrictions.)

Additionally, if a Nintendo Network ID is linked to both a Wii U and a Nintendo 3DS, the Nintendo eShop balance is consolidated and shared between them.

All free software demos downloaded prior to linking a Nintendo Network ID.

Putting all of this together, it is reasonable to say that:

• As long as you put the game onto your SD card, it will not be deleted if you follow directions during the transfer.
• Because the new system is not associated with a Nintendo ID, you can transfer everything from your old 3DS to your new one without any problems.
• You can transfer over your Nintendo ID to the new system and, as long as you don't reformat the SD card, you'll still have the game.

The New 3DS and its XL counterpart both offer only 1 GB of storage space. Pokémon X/Y and Pokémon ORAS require 1.7/1.8 GB respectively. Obviously, each game is far too large to fit on the 3DS' internal memory.

Fortunately, the New 3DS supports SD cards to extend the console's memory, and ship with 4 GB SD cards by default. However, it's possible that games require more free space to install than they'd occupy in memory. The Wii U, for instance, needs roughly twice the space to download a game, then decompress and install it. This would explain why you could install AS (and its update), but not X.

The only way to fix this, is to buy a bigger SD card and install it into your 3DS. Unlike the original 3DS, the New 3DS supports Micro SD cards instead of the regular ones. Make sure you buy the correct format, or your new purchase won't fit inside your 3DS.

Keep in mind, that although the New 3DS supports SDXC cards (which offer capacities beyond 32 GB), you can't just insert SD cards larger than 32 GB and expect them to work out of the box. SDXC cards with capacities greater than 32 GB are formatted using exFAT, which the 3DS can not read. To use 64 GB cards or greater, you'll need to format your SD card using FAT32 instead.