The problem - messages on default skin include project name, and the
inclusion costs milliseconds. I didn't do proper profiling now, but
it may consume up to 20% of time required to push out a simple page.
The easy immediate cure for any site is to check that there're no
transformations happening in these messages:
As for mediawiki development, the urls may point to Project: (what
would be rewritten into proper project namespace afterwards), or have
$wgSitename used in Message files...
Message transformations matter in many other cases, but those at
least are not triggered on every page load.
I guess this doesn't matter that much with Tim's new Skin rendering
engine, but I can't tell now, :)