I've finally decided on how I'll deal with the story vs exploration problem in 100RTBD. It's quite simple, really! As I'm making the side rooms and the optional paths, I have to ask myself if the player should be allowed to progress or to stumble into a boss fight or something at the point he is in the story. In most cases, the answer is no; You can't fight the second version of a boss if you haven't fought the first, for instance.
So if you get into such a room and you see "Something is missing... Come back later", that means you'll be coming back to that place sometime in the future. For now, it's a good compromise.
Time spent on the project so far: 584 hours
Currently working on: Making side areas