Kohana is a little brain-damaged. Good intentions, but it's essentially a PHP5 version of CodeIgniter in most ways that matter. The problem with this is that a PHP5 version of CodeIgniter doesn't leverage the constructs and concepts that make PHP5.3 (which in 2011 is the lowest version of PHP you should be considering) much more pleasant to work with than previous iterations. Kohana, and CI2, are both rather meat-axey frameworks, where the trend is toward elegance.

I'd consider Symfony2 for most applications, or Silex (which is the Symfony2 app kernel, stripped of the majority of the Symfony2 framework) if you like writing the plumbing yourself. Yii is pretty nice, too.