Marathon used a different system of level-building (portals instead of BSPs) that let you stack levels vertically, so it's actually possible to create a lot of nice architecture with some good view faking. Also, it's one of the few games with a good story, and maybe the only FPS.

There is one major thing missing for constructing a "modern" game with it, and that's scripting - the open source version has Lua, but I don't know if anyone's written anything amazing with it.

3rd party scenarios for Marathon were also oddly literary, like this one where you go back in time and save Leonardo da Vinci from aliens.

http://nardo.bungie.org/alephone.php