Would you like a fork of the Atahualpa Theme? Read on!
I think there are many (like me) that echo your last thoughts. Nonetheless, even with the patch or fix, Atahualpa is still one of or perhaps the best theme for MultiSite installs and Multi Networks.
We have it working, in production, on a network of more than 3 dozen sites.
In fact it works so well, a few people are talking about a fork of Atahualpa, humorously referred to as "To Code!"
If you are interested in this, perhaps you would add a comment about a problem or feature you would like to see resolved/added to "To Code".
Let me stress, EVERY ISSUE addressed in this thread (as well as a number that are not) are already resolved in the "To Code" Fork and it is running on a number of network sites.
This Mature Code was offered to the developers of Atahualpa for each of the last seven releases. It has not only been rejected, most threads about it on their "support" forum have been deleted.
Recently the support forum was changed from free to a paid basis.
The main developer is working on a new PAID Theme. Since the beta of the paid theme was released, Atahualpa has not been actively developed. In fact a number of newer releases (problem fixes) have actually lost features.
These are all reasons to support the "To Code" Fork or we all may be shelling out 160 bucks for paid "Atahualpa Like" Theme.