Reading Kohana's documentation, I found out that the main difference in 3.0 version is that it follows the HMVC pattern instead of MVC as version 2.x does. The page about this in Kohana's docs and the one on wikipedia didn't really give me a clear idea.
So question: what is the HMVC pattern and how does it differ from MVC?
Sam de Freyssinet (one of the Kohana developers) wrote a rather in-depth article about HMVC, what it is, and how it can be used.
Link is dead: New Link - https://web.archive.org/web/20160214073806/http://techportal.inviqa.com/2010/02/22/scaling-web-applications-with-hmvc/