1. The first boss is too easy to kill because you can sit behind the crates that he is constrained by and then pop up and down to kill him. How about he only appears once you are in the area he fights in?
2. The bullets don't damage you once you kill the enemy that fired them (although I think you know this one)... makes the level too easy - hold space and run forward.
3. The boss on level 2 is sooo random... it's almost impossible not to lose any lifes because you can't move quick enough to keep a safe distance incase he decides to charge after jumping. How about a short animation between changing modes so you can move to safety or up close to kill him. Are grenades going to make him easy e.g. sit on the top of the wall and drop grenades.
How about a level timer so you can see how quickly you did it in, my favourite thing in blocky was speed running the levels against friends (could do the first 3 levels without releasing the forward key)