* Their wild pile of oddly-named functions are being deprecated and moved into well-designed classes.
* Better templating options are being promoted.
* Yes, the global $wp_query leaves some to be desired, but at its core, wpdb's WP_Query is a decently powerful database abstraction, and if used right can perform well at scale.
No, the hooks aren't going away, nor is the URL-to-template mapping. But those are the parts that make it so flexible and easy to work with. MVC is a controller dictatorship, WP's code is a democracy.