I bought Thesis with intent to use it on my next project but gave up due to multiple inflexibilities.
It is an excellent general purpose blog theme with careful attention paid to SEO features and basic customizations.
Right off the bat is look nice.
What turned me off if inability to create multi-level navigation menus for it.
I compensated for it and even created an multilevel nested custom navigation for Thesis theme tutorial
But Thesis does not support fluid layouts and to customize CSS you have to go and edit it's custom.css file directly. Additionally to that to customize functionality you have to get your hands dirty and edit custom_functions.php directly as well.
With Atahualpa you don't need this - everything could be done via admin panel, including PHP inserts - which is great.
Plus with Atahualpa you can customize 1000 more things that neither Thesis nor other themes are even coming close.
Thesis is great for totally non technical webmaster who wants working and nice looking blog right off the bat and doesn't mind looking like twin to thousand other blogs.
It's not exactly me - so I reverted back to Atahualpa.
I still decided to customize Atahualpa's navigation menu - see my new vga capture
site with custom menu. It's a bit less work to do compare to Thesis.
Hope my brief comparison helps a bit.