Yeah most of the US Pikachu 3DSXLs are gone and the only real chance of getting one now is through sites like eBay. I ordered mine through Toys R Us online due to some stores in my area not even getting one along with way too many eBay/Craigslist people visiting my area just to buy and resell it.
If anyone here (in the US) went with ordering online you can always try/call and see if a local (Target/Walmart/Toys R Us, store you bought it with) will give you the price difference. My local Toys R Us told me if my system arrives before this week ends and I bring that Target ad along they will give me the price difference (I have no clue if its cash/refunded credit/store card or gift card though).