I will be purchasing my own 3DS here sometime in the future (preparing for PokeGOD, of course) and I've heard pros and cons for both, most people saying that the XL is better. While I know it may be minor, I really hate that the graphics could be cloudier because of the bigger screen but not bigger resolution.
I only have the regular without having played the XL, but I'd note that when playing non-3D games on even the regular (assuming you plan to ever do so), the graphics are cloudy and not as sharp, a problem which my be exacerbated by the XL.
3D games look perfect on the 3DS, so I don't imagine the XL would damage their graphical quality that noticeably.
You'd be fine with XL - I think the resolution was optimised for the XL.
The reason DS games look blurry on 3DS screens is due to the 3DS's increased resolution, but the screen is only a tinier bit bigger than the DS screen.
I wish I had an XL but I'm not about to trade my Zelda 3DS in any time soon.
XL. I was worried about pixelation/resolution issues as well, but I've had nothing but positives when it comes to 3DS games. There is some optimization. I've no doubt that XY will look better on the bigger screen.
As far as the old generations go, I always hold start + select as the game loads to shrink screen sizes on the 3DS models (original OR XL) just because I prefer the classic Pokémon style to be as crisp as possible and not blurry/pixelated. Both 3DS models will give you some level of added pixelation + blurriness on DS games.
Finally, as others have pointed out, the battery life is a huge plus.
