I've worked with Kohana a lot and I really don't like it, besides how skinny it is (oh, and the H in HMVC). Weird thing is the best programmer I know recommended it to me.
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.
Kohana also has the worst documentation in the world. Seriously. It has very clear comments in its source code, though.
(I still wouldn't use it because frankly, I don't think the Kohana developers take security seriously enough, but it'd be a start.)