It was ok, but not too exciting
Graphics & animation were good, but it just got boring too fast. Joe trudges around slowly, and you do the rat-maze routine trying to figure out where to go. The machine gun was about as useful as a tick on a dog's ass while the shotgun was far more powerful (never overheated, and had a good spread). Flamethrower was pretty obscene, too, but overheated very fast. Fully upgraded shotgun was by far the best weapon.
The upgrade system seems redundant in that you have to get xp to pay for things, AND you need vials just to do an upgrade. Just pick a system and go with it. Either make user collect xp OR vials. The way you have it just adds in unnecessary complexity for complexitiy's sake.
I think you'll find that since Left 4 Dead came out, nobody can do a zombie game and expect high scores on NewGrounds for some time to come. Everyone's going to expect this to operate like a top-down version of Left 4 Dead, and they'll skip the intro so they won't know the background to put things into perspective. I think you did a good job, it just gets too repetitious quickly and bores easily. Then again, I'm an older gamer who's played way too many games like this (that's not me bragging, it's just me stating that the older you get, the less novel things like this become). For younger gamers it will probably still be pretty fresh.