Here is what I ended up with at the end of GGJ 2012. I've cleaned it up a bit, got it working under Internet Explorer (mostly) and put it online here.
I ended up with more of a virtual world or virtual ecosystem than a video game. I ran out of time to put probably the most important thing into the game - game mechanics. Also no time for sound, the player has very little agency in the world, and there are no win or lose conditions.
Overall it was a lot of fun to build though, and I got some pretty neat new technology for jsGameSoup out of it, namely the isometric camera library, and a lightweight vector math library.
GGJ was also really fun just because of the social aspect of being crammed into a room with like minded people for 48 hours. Can't wait for next year!