Awesome idea. I like the main mechanics and the power ups you gain when you progress.
Here are some suggestions:
Make the player walk faster. I think he walks a bit too slow.
When level is finished you could let player to advance to the next level without mouse. It is a small thing but I felt it a bit frustrating. :)
It would make gaming experience more fun if you could make clones more predictable. Now they are messing with each other and if you push some of them they try to continue walking the prerecorded path and end up being in a wrong spot. Maybe you could disable collision when they move and enable it after they have finished moving. But that wouldn't work because you need them to help on the go also. It is a difficult question... Something has to be done, but what? I can't help you. You have to re-think the mechanics somehow.
But don't get me wrong. I had really fun playing your game. Keep it up! :)