I have 5 copies of the downloadable version of Art Academy spread out over my various DSes, and I still couldn't wait for this version for the 3DS. It has so much more content - Colour pencils (which I always wanted), pastels (which I can't wait to try) and more lessons, plus there will be downloadable lessons. You can pick from different textures of paper, and start off with colour paper instead of a white background. The paint even has a 3D look to the texture, it's not so flat like before.
The paint tray is larger, and has a much larger selection of colours, including pallets of colours that work well together. I noticed that in the pencils and pastels as well, though I haven't had time to try them out.
There's a "gallery" to show off your work which is nice. It's like walking through The British Art Museum where you can hang your art on the walls in the many rooms. It's an easy way to show people your work without having to look for it on the SD card. It looks like you can also share art via Street Pass, but I'm not sure how that works yet.
And a really nice feature is the stock images of photos for you to draw from. They are in 3D so look very real. The still life photos let you rotate the light source the way you think looks best. And there are some 'live' photos as well, like moving rivers and wind blowing through the trees in landscapes that make it feel like you're painting from real life. All in all, this is a GREAT version.