Well done
I give this animation a 9 for how damn solid it is. That is, no one part is exceptional, but as a whole it really stands out. As strange as it may sound, a lot of artists modify the script and direction to fit what is easily done. I do it a lot myself when confronted with difficult shots. You don't seem to have held back with this, and I really like that. I'll break this down and be a little bit more specific than I normally am.
Audio:
The music did its job and didn't stand in the way. Nothing took place that really could have gained much more power from some overused Hans Zimmer music, so no faults there. The sound effects were a little over compressed in some cases, but such is the result of a megabyte budget.
I disagree with many other reviews. I felt the voice acting was reasonable, and above the common standard of newgrounds. Yes there are some AMAZING voice actors and actresses out there, some of which I've been lucky enough to work with, but its just physically impossible for every single animation to have top notch VAs. I thought the acting was just fine. The quality of the samples was lacking, but again, this is out of your hands.
Just so you know, the secret to good VAs is puting your idea out there, asking for auditions, and poking around in places like the Voice Actor Alliance forums.
Animation:
Movement wise, again, you've done as much, if not a little more, than was necessary to imply movement. All animation is implied movement to some degree, and with a budget of zero dollars, extensive frame by frame sequences are just plane unrealistic expectations. This is obviously a character driven story, so writing and still visuals takes priority.
On that subject, I would recommend, as some others have, that you try using the paintbrush tool instead of vector lines. The brush does a better job interpolating your intended strokes (a godsend if you use a mouse), and overall looks cleaner if used properly. If you really spent a year on this, I'd say its worth your money to invest in a WACOM tablet if you haven't already.
You characters could use a little work. I think you just need to spend a little more time on them, and need carefully drawn character reference sheets. When artists draw real humans, they often use real human references. You should consider picking a studio or artist who draws in your preferred style, and start using their artwork as a reference for your own. And if people dislike your work because it is Anime styled, screw em. There is a reason why Anime is the top grossing style of animation. Its simple enough to be affordable to draw, but stylized in a way that makes its characters enjoyable.
Your 3D animation isn't mind-blowing, but it more than does its job. I really like how it is employed. I never received any 'formal training' in 3D art either, but I'm now able to illustrate complex transforming flying vehicles. Its just a matter of dedication. I can see you are modeling with primitives for the most part. I'd recommend you pick up a copy of Milkshape 3D ($20) or Blender (Free) and learn the art of 'extrusion modeling.' That'll allow you to make more complex shapes, and interesting things. Swift's interface is meant for posing and setting up shots, and its a terrible modeler. You might also be able to use Sketchup, but you'll need PRO to export .3ds.
Story:
Your dialog was well written (especially by newgrounds standards) and the story complex and original. I'll admit I was kinda lost, like watching the 5th episode of a 13 episode series, but you've been told that already, so I'll leave it be.
Sub titles would be great. I know in the elevator scene, I was unable to make out what was being said over the SFX in a shot or two. I don't understand what you mean when you say 'program' subtitles. I've subtitled the majority of my work, and I don't know a single line of ActionScript.
Its a simple process of adding a text layer and timing it with your audio. This is even easier if you use the text as a trigger for the vocal files.