New Nintendo 3DS is basically an upgrade to the older 3DS and 2DS models. You'll benefit faster processor speed for executing certain operations significantly quicker, and also let you play several New 3DS and SNES VC games in addition to the already meaty library.
In the older 3DS models, the 3D effect tend to be ruined by just slightly tilting your head. The New 3DS models solve the issue by enabling face-tracking to adjust the effect on the fly.
Exclusive to the smaller New 3DS models, are the interchangeable cover plates. Both of the upper and bottom cover plates are placed by pushing them into the system, although the latter requires a Philips 00 Screwdriver. You use the larger tip of the stylus in order to pry the covers off the handheld.
Oh, and the microSD card compartment is covered by the bottom cover plate. Though, you could also use a wireless router and a computer to access data from the microSD card.