Having gotten my 3DS XL yesterday and I had problems at first with getting the games from my old 3DS (the bottom screen on my 3DS became black/broke). I finally got everything to transfer (especially the eShop license, which allowed me to download my old games). The actual games didn't transfer and I think Nintendo really needs to revamp how they do eShop a bit a la PS+ (either that or I didn't select the right option on the original 3DS). You upload the save data to eShop and download it along with the games but that's just me. And it's tied to your account, not the physical hardware.
Anyway, the 3DS XL is so much better in every conceivable way. Although it feels more like a toy than the original 3DS, it fits more comfortably in my hands and the screen size makes it easier to play games. I played Theatrhythm last night and I could tell the difference. I was having an easier time playing the Expert battle tracks, which wasn't the case with the original 3DS.
Overall, I would say it's a better system than the 3DS and I'm somewhat bitter about the fact that my launch 3DS didn't last as long as I wanted.