Really nice! The template system is small but still efficient, you can tell that you thought this through. Although one thing I would like to note for you.
Instead of defining a directory separator you can just use '/' since it works on both *nix and Windows.
Also, generally when writing MVC applications and I come to the settings part, now this way you're doing it works. But it would be way more comprehensive to use the default PHP INI system and use parse_ini_file on this instead into a multi dimensional array.