I don't know how you and your websites cope with it, but as much as I like atahualpa for its adaptibility and options, as much I hate it for it's abuse of CPU Cycles and queries.
Using wordpress default theme I can get by with around 50 queries per pageview with all my plugins activated. Going for atahualpa this goes up to 120 queries on 3.3.4 or 160 queries with 3.4.1
Simply said it's a disaster and doubles the time to build a site. This goes so far that even with wp-superchache in full on or bad behaviour on and wp-supercache half-on in the evening my dedicated server crashes (celeron 2.8 ghz, 1GB Ram, running Suse and 2.6.29 kernel).
My site ( www.openmtbmap.org ) gets currently bout 10.000 pageviews a day, so this should not be a big problem.
However with each atahualpa version cpu-use got more devastating leading to a lot downtime of my site.
Is anyone actually running atahualpa on a page with say 10.000 visitors a day without getting problems with CPU usage? I got banned from my first hoster for cpu-usage and now I have problems keeping my own server from crashing.
Atahualpa is the main culprit for this. I have tried out more or less any cpu wordpress optimization guide, but using atahualpa seems to be attacking from the wrong side. Because over 10.000.000 database queries each day are simply too much for a simple site.
inline vs external css options showed no improvements at all.