I am already working on a completely new backend for Atahualpa 4.0 that uses the new WP Settings API, it will have direct image uploads, and image sorting with drag & drop, and everything will be saved in the WP Uploads folder.

Making the transition smooth for 3.X users will be the tough part. There's quite a bit in Atahualpa that I'd like to replace. The code base is 3 years old now, and other themes have catched up

I am mainly concerned about how much I'd alienate current Atahualpa users if the upgrade breaks a couple things. With custom CSS etc. I see no way to make this absolutely painless.