A problem with the current version of Atahualpa is that, when automatically updating to a new version, all extra files added to the theme subfolders are lost. This is escpecially important for the images/headers folder, where we store the header images.
Since a long time now, WordPress core have had a function to add custom headers images. This is elegantly used by the default theme, Twenty Eleven. When you upload header images, those go into the media library and are tagged header images. They will then not only survive an automatic update of the theme, but will even show up when you change to another theme supporting custom headers.
Currently, Atahualpa insist on doing theme options it's own, proprietary way. This mostly done by an elegant and nice options page, but also quite un-elegantly by simply deleting and/or uploading images by FTP. There may have been good reasons for that approach in the past.
For future versions I hope Atahualpa will move in the direction of utilizing the core functions of WordPress, in those areas where there are core functions.
The new default themes where made of two reasons: One, to have a nice and decent theme for the first time user, and second, to educate theme authors in the latest core functions and how they might be used in modern themes.
I want to stay with Atahualpa, as the most easily and elegantly customizable WP theme on the planet. But I must admin that I have chosen to customize Twenty Eleven using a child theme, for some of my latest projects. The main reason is that Atahualpa is lagging behind in respect of todays WordPress, and that automatic update must be warned against for most end users. This is a bit hard to communicate, because I advice to automatically update anything else than Atahualpa.
Last: There are some more core features that Atahualpa currently ignores, like post formats and post thumbnails. Find a use for those, too, please.