Oh awesome, thanks for the great feedback! A lot of the things you mentioned were already on my to-do list but it's good to have that second opinion to show I'm going in the right direction.
You've given me some good ideas for some different characters as well, I hadn't thought of that; I might put in a couple of good characters that drop powerups or give you a shield or something.
I will be working on making it more obvious when you're damaged, the cracks that are in there now are actually leftovers from a previous incarnation of the ship. Dents are a good idea too.
It is difficult to show whether the bacteria or the ship will be damaged... I'll try implementing your suggestions, I also thought maybe I'll change the expression on the face of Dr Wiggi, make him look scared if they're coming from above or something. I may change the way collisions are detected too.
Different levels are a good idea, I wasn't sure whether I was going to continue to develop this game or just submit it and try something new, but since it seems like it will have a good chance I'll work to expand it a bit, perhaps have a map of the patient's body that the Dr is working his way through so there's some progression in there, with different backgrounds and characters each step of the way.
Thanks heaps for your feedback!