I commend you for having an animation as long as that with everything done by yourself. It's no easy feat creating CG animations at are even a minute long, let alone over 3. It's in sort of a strange middle ground though.
You don't use subdivision modelling for any of your characters, so we can see the poly-flow, and all your textures are very flat, with your shaders limited to lamberts and maybe a few blinns here and there. That would be all well and good if you were trying to show off your animation skills, but for the most part it's lacking - especially in the running scenes. Your facial animation also seems a bit robotic, and limited basically to the eyes/eyebrows, and maybe a bit of mouth. Given the scale of the project, it would be too hard to get good blend shapes or facial rigs for the 20+ characters you have, which is understandable. Also, your lighting is frequently inconsistent (shadows are cast directly behind the main character (and sometimes has two shadows for no apparent reason), your shadows are extremely sharp, and you might even be using an ambient light, which you should pretty much never do.
So basically, since your aren't showing off your modeling skills, lighting skills, texturing skills, or your animation skills, the story is the main focus. The story is definitely interesting, but has some holes. How did that guy wake up in the woods, why was he in a world filled with zombies, and if it was just a bed-time story told to a kid, why is it shown that he actually exists in the end? Also, you have some strange cuts, like when he runs from the diner he's immediately in the middle of the road around the corner. There are some strange slow pans as well, and you don't have enough easing in and out of your camera. Also, completely off topic, you have some parts that are super reflective, which is a common mistake.
I'm not sure what you want from this animation, since it's scale is too large to focus on any one thing enough to make it stand out. Since I can't imagine your render times are longer than maybe 5-10 seconds a frame (or less), it could be really easy to go back in and fix up shadow inconsistencies and mess with camera movements/cuts. Depending on your rigs it might also be semi-easy to really clean up the animation. You can't really do much else to improve it, since you clearly chose a limited style with very basic shapes and textures/shaders. So there's no point in doing global illumination, subsurface scattering, color bleed, or any of that fun stuff. Maybe do an ambient occlusion pass. That generally makes everything look better, and would not be hard to add in post.
So there is my two cents. I just finished the graduate program at Drexel in Digital Media by the way, and teach this kind of stuff. Take from it what you will, and don't think I'm trashing your animation. I'm just used to giving a lot of critiques. Good luck with your stuff.