Which one do you imagine to be rarer? The X & Y 3DS XLs or the Limited Edition Pikachu ones?
Rarer ones = the Japanese Pokemon Center exclusive (non-worldwide release) 3DS LL units, either the Charizard or Eevee, or even the Gold version X&Y. Each of the Japanese exclusives had either strict limited #s given away by raffle only, or only limited posted official quantity made available.
As for value, New In box will always remain valuable, but so far it looks like the Charizard limited edition is the rarest and most desired, current and past sold ebay listings are the most for that version, $400-600, other limited editions such as the pikachu, eevee, etc all are about $400-500 for sealed in box, while 200-400 open out of box depending on condition and luck.
So all I can say about the limited edition pokemon XLs is, as long as 3ds xl is the current platform by Nintendo (isnt replaced by a newer/better handheld console), opened units will always retain some value over their regular counterparts, anywhere up to $50-100, but new sealed in box is when you can hit 100-300+ in extra value. However much like the Older DS and DSi units, etc, when the 3DSXL units came out and were the successor, those limited edition units took a $100+ drop as their "mass" desirability took a nose dive, only desired by "collectors".
Better than a Bank Savings account, if you want to save money, have money to keep in assets, want to up to double your investment, buy out these limited edition units, keep them stored away safely to retain mint sealed condition, and in as soon as 4-6 months time, you can cash out and sell for up to double. Too bad I don't have hundreds laying around to sit on in invested assets or else I would do this :)
Also to be honest, I'm not quite sure how rare these X&Y limited edition units are, not sure if Nintendo stated anywhere how many will be made, but this time around, it seems like every major retailer has it, Best Buy, Target, Walmart, Gamestop, Toys R Us, and not to mention countless smaller shops in N. Americ, so I'd imagine there had to be upwards to thousand+ units made for the pre-release alone, and even now that it's released.. Stores which were "Out of Stock" during pre-order, such as Gamestop, Best Buy, Fry's Electronics, are now Back in Stock and available for normal purchase.
Even Gamestop has dropped the word "Limited" from their product page's title and description. So would appear that maybe they know these aren't "Limited Edition" with no official word to say when Nintendo may stop making the units or limited to certain number.. Even their product page for the Pikachu 3DS XL still says Limited Edition (albeit soldout).
https://www.gamestop.com/browse?nav=16k-3-pokemon+3ds+xl,28zu0
So they may just be Limited Edition solely based on the fact they are a special 3DS XL unit, but in no way are they rare, as there's no official limit to how many were made and with being available around the world including Europe, rather than a Japan and/or N. American exclusive, probably pushes their numbers up to the hundred thousand range.