I concur that there is no need for .inc file extensions and have already changed mine to .php. So I agree there is no need for Fat-Free to do this.
And yes, having built a large application with Drupal over a year (3 years total including other sites) and seeing how thin what I have done in Fat-Free in less than 2 weeks is is a huge contrast!
Unless you want to build a site using a UI heavy CMS, with tons of 3rd party modules, and enjoy keeping up with their updates, and hacking things to work the way you need them to work then Drupal is not for you. When I first started working with the rendering engine I was impressed and after all the bloated field configuration and building a large set of wrappers to streamline things I am now finding that it was all a huge waste of time. The caching in the rendering engine was also very enticing but Fat-Free already provides that and caching in multiple other areas to boot.
No need to argue one way or the other but yes in hindsight a lot of things in Drupal appear silly IMHO as well... but for the developer that primarily cobbles things together it may be quite useful.
--Nikolaos