I remember this contest. I didn't get as enthused about it at the time...
About the only difference that I can see between yours and the winning designs was an option of color. On a lark, I kept your black border and perspective shot as is, but I inverted the black-lines to white-line isometrics.
The parchment paper actually gave the illusion of space to a degree... I wonder if that would have been a more favorable presentation to make yours a winner??
Maybe I can help here's a [link] to a tutorial I made awhile ago. Some people have found it useful. It deals about how to design a mech, but the basic principles can be applied to all sorts of design- themes. Good luck!
Ah that's a good position to put it I've seen many bridges in weird locations mostly the center of the hull on the top is the best but I have seen some that are on top of massive spires and the Pillar of Autumn from Halo 1 had a very bad bridge location it was on the front side of the ship but instead of on the top it was on the bottom which wasn't good because they had to crash land it guess what goes first, ya that's right the bridge so basically all of the people on the bridge got killed once the ship hit the ground except for Keyes!