Very, very good.
I like the music. A little grip would be that the Prophet doesn't have a name, but then, maybe it works better that way.
The levels are nicely done. Due to my personal preferences, I vastly prefer Dead Gulch over Area 51 and the World of Machines. I will, however, admit that the Machines world was done very nicely and humorly, what with time warps and what not. I really liked the humor in all stages however.
The enemies are basicaly all the same, with different looks. Maybe the machines and alien foot soldiers have a longer reach then zombies. Don't know if this was intentional or I just saw it wrong. It doesn't really matter, since it ruins nothing.
One thing I liked very much is how enemies work in unison. The meatshields harras you all the time, while the artilery throws everything it's got at you. Makes you change your places and adapt to situation at hand, which is only good. And it can work in your favor, once you figure out that enemies can be hurt by ranged attacks from their own guys as well. AI seemed quite intelligent, adapting to situation somewhat. Don't know if it was random or programmed, but it was nice to see. This is a game that doesn't spare you and I count that as big plus.
Weapons look nice and useful. Haven't tried Alienator yet, but crowbar and Cyber Blade are great weapons, one as mighty offense and the other as potent defense. Nice touch that you can't gain special attack power while under the influence of the shield, the potential for abuse is great there. But I'm not really sure what's with Zomboss's arm. Was it supposed to make the attack more powerful? The description certainly says so, but I'm not seeing it. Or I'm seeing it too little. Not saying it's bugged, but I have that feeling.
Bosses are too easy, once you figure out what the trick to them is. Especially Smiley. However, Smiley later gets "minions"... of a sort. I think Zomboss and ZOMG would do well to have few minions as well. Would make the challenge much more potent and the satisfaction at beating them that much bigger.
Love the medals, got 10 of them in two playthroughs. I imagine Anorexic will be the hardest one to get, but with right use of crowbar, nothing that can't be done.
And like cega0 mentioned, the stun(even if it only lasts for a part of the second) is very hard on a player. The enemies swarm you very quickly and you die fast. Either add checkpoint or somehow disable the stun effect from the enemy hit.
tl;dr: it was a great game and I enjoyed playing it greatly. Hope to see out Propher again.