On the NerdMom blog there's a recent post from Jen about her experiences in developing in both the CodeIgniter 2 framework and Kohana 3 frameworks (upcoming versions of both).

For the last month or so I've been developing an app side-by-side with Kohana 3 and CodeIgniter 2 to see which framework fits my programming style better. Nothing terribly fancy; just a simple CMS. [...] In the end it comes down to framework stability for me. And in this case, CI wins, hands down. Don't get me wrong; Kohana is beautifully written and introduced me to a prime example of clean, well commented code.

She talks about some of what she was needing out of a framework and what ultimately lead her to pick CodeIgniter 2 as the tool for her and her development. She notes that, while Kohana is nicely written, they've had some consistency issues with backwards compatibility that have caused issues. She also mentions some of the unstable code that was added just to micro-optimize things when it wasn't needed.