One of the most important aspects of a PHP framework to me is the ease with which you can add or swap out libraries - and being able to include things with Composer and use its autoloading features would make a framework more modular and easier to manage and extend in the future.
Having your own extension system is fine and perfectly valid, but a lot of people have already invested in the existing package manager and PSR-0, and will expect to be able to use it in for their projects.
As far as the rest of it, I would mention the use of the deprecated (and highly vulnerable) sql_* functions and the lack of xss protection in the templates but I assume changes to those would be forthcoming.
I like the lack of abstraction and the built-in MVC, though I think people used to Rails-style routers in other frameworks like Laravel might wind up a bit put off.