Ah I forgot to mention that a timer is already in the plan! I like your suggestions though. We might be able to get something like what you describe into the game.
The challenge missions would certainly not be required but would unlock stuff so it's up to the player.
I don't think you should worry about console degrading the PC version. We should be able to manage to get both working effectively especially since i want to support gamepad on PC. For indie game developers you really have no choice but to try to release on multiple platforms these days. You just can't rely on Steam only. The only way I can keep making this and other games is to have this one do well!