Well done!
Definitely an interesting idea, and it's nice to see that you've developed upon it. I enjoyed the upgrades system but think that you need to better the intro. The intro itself is fine, but seeing as the game's name starts with 'Auto' I thought for a minute that it meant automatic. Just a simple black screen with the words 'One day..' etc. would probably solve this for me.
I did however encounter a few bugs. The upgrades screen would reopen almost every time I tried to close it(This obviously got a bit annoying). Then my game play was halted when my character jumped in the air after dying, and did not return to show the main menu.
Overall I loved it, being a 3D games developer myself, it's nice to see someone working in flash, truely unique.