Kohana 2 was "just a php5 fork of CI", while Kohana 3 is practically a whole new framework. The "problem" is that Kohana team doesn't like handicaping new versions for sake of complete backward compatibility.

They just make the framework better with every new version, although in case of Ko3 minor versions are backward compatible (for example 3.0.8 with 3.0.1., but 3.1.0 will not be, at least concerning the response object and the ORM logics).