Some of the challenge room are pretty straightforward; kill X enemies under Y seconds, some of them are a bit more involved than that, such as the last one I've just made. You have to get to the end of the room in under 30 seconds and there are plenty of enemies about. Killing them all probably would be safer, but it will also make it difficult to get there under the allowed time.
In my design doc, I didn't plan for the game to be really difficult and this particular challenge room didn't have any rewards to give, now it's giving a small healing item, because hey, let's be fair with the players, if I'm having trouble keeping my life, they probably will too.
Another small issue I tackled is the way players can skip certain parts of the game or go out of order, I fixed that by unlocking certain things no matter what after a while, so it won't break the game too much if you decide you don't want the bonus damage from the gun part in that first challenge room.
Currently working on: Continuing the story
Time spent on the project so far: 110 hours
Screenshot 34 after the jump: A small challenge