If you are having trouble in the later levels use a sleeper block tower closest to the portals facing the toys with a sticky block tower closest to them!
The annoying thing is-
I have left the game idle as it can and three times now, I have come back an hour or two later and i have found all my team attacking a floating skull with millions of health that keeps leveling up and regenerating health...
I think there should be a timer you can set to fail the level if you are attacking the same enemy for more than 2 mins or so!
Upgrade restrictions are not a good idea in my mind, but I understand why. I think you should be able to lift all upgrade restrictions when you beat the level in hard mode.