Somewhat finicky controls, but aside that.. This is easily, in my mind, going to be a popular classic later on. Even withstanding the limited guns, and upgrades, it's actually very fun; Upgrades never felt too strong, each gun had it's own uses, and if you conserved health and food, you would be able to purchase much more if you went in heads on. Plus, achievements in this happened to be surprisingly fun, albeit not difficult in the slightest.
Cons; AI, happened to be horrid for me, peculiarly in the final level. Since I was going for the savior medal, well.. Each of them kept bustling out, and died as a result. In the sequel, (Since this definitely warrants a sequel of some sort, by the game itself and such feedback) I hope they happen to be less jumpy, but not static. Secrets, while limited due to the platforming aspect, were sometimes well hidden, but all you needed to do was search for a while.
Somewhat disappointed that man v.s man wasn't an option, though. Fighting against fellow, rouge survivors might'ave been quite fun, just an addition to the alien aspect. Never did this game take itself too seriously, and while the premise is cheezy at times, for a flash game, very impressive. Now, I was a little disappointed about the lack of guns; Flamethrower was a very neat addition, however, so I'll give you that.
All in all, it was thoroughly enjoyable, save for the AI. Even backtracking isn't tedious, since it encourages finding lost items.. Now, though, the gas mask might need some tweaks. After an upgrade, just one, you essentially never need to buy that many, which is saddening to me. Perhaps that could be tweaked in the sequel, as well, maybe if you sustain a certain amount of damage, your mask will consume air quicker? Just a suggestion.
Good job!