Go for it! Just keep in mind that there are certainly more titles on the way that will be exclusive to the New3DS. Who knows how many or at what intervals they'll be released but I highly doubt Ninty made a system with more RAM and power capabilities for one game, as beloved as the game may be. If you're cool with that, then hellz yeah, get to catchin' those monsters! I agree, I'm perfectly happy with my 3DSXL (even though I'm definitely upgrading) and I've got about 160 hours on my Pokemon X game. I've never had that amount of hours in any game, even in the past (scratch that, SOCOM 2 I think I had 200+). Suffice it to say, it's worth it if you're a big Pokemon fan like myself; and with Omega Ruby and Alpha Sapphire coming out in November, it's a great time to get started on that X/Y file and then move right on to Ruby/Sapphire! Not to mention trading Pokemon between games is easier than ever these days. It's great, Ninty has pretty damn close to perfecting the "Pokemon world" feeling. It's funny, that's even transitioned into the real world. Tournaments are friggin' awesome these days.
I digress. DO IT!