Kentico 12(Raptor) is "MVC first" approach. That means that all new features will be developed with MVC first and then with the portal engine if Kentico decide to do so. There is a big shift towards MVC. Kentico 12 release is not that far (Dec 27 the date I heard at the connection). That being said you could start with Kentico 12 beta and then release your new site with Kentico 12 release.
It is not recommended to mix MVC and portal engine (Although I've seen that). With Kentico 11 it is usually 2 web site/app setup. There articles here and on MVP sites. If you planning on developing a new site - start with beta version and 2 web site setup.