After reading this article, I opened up System Preferences on an external WQHD monitor and... yes, indeed. That transition is not very smooth. Informally, it doesn't seem slower ...it's just not as smooth as the old effect.
As another poster noted, in Yosemite those panels now use a cross-dissolve effect instead the simpler slide and fade in earlier versions of OSX.
Thing is, I'm not sure I would have noticed this in a million years.
How much time do you guys spend clicking around in System Preferences every day? This really affects you?
I don't know of any other apps with preference panes that use this effect. I tried two other apps (iTunes and Pages) and neither one uses the cross dissolve.
I understand that this small regression is merely emblematic of the issues some of you are experiencing; none of you are claiming that System Preferences itself has a huge impact on your daily lives. But this is such a ridiculous regression to select as the poster child for Yosemite's perceived woes.