Great link. I've actually been to that site before, but never read that article in its entirety.
Some selected quotes from your link:
Imagine the bounding/perspective box in your head and draw the closest edges and details first so the overlaps work out. Stick to a theme (square, pointy, curved). The more themes you mix and the more stuff you tack on... the less identity the design has, I feel. Two large piles of junk don't have as much identity as maybe 3 pieces of junk from each pile stuck together.
It can be a risky endeavor to go for l/r asymmetry, and I think it's because the human mind is used to the top/bottom, back/front looking different on humans. Our minds are instinctively opposed to l/r asymmetry so a designer probably needs some kind of special justification for it, or time to let it grow on the viewer. If you go for it, you have to think carefully about which elements that you offset from the center, escpecially where the engines and recoil-guns go (if any). Sometimes even a hint of imbalance can be enough to annoy.
A ship that's just shape-play is not that interesting. It needs... a thing... some quirk, some features.
He has many interesting links on his site, X-com, Master of Orion, Star Control 2, Amiga stuff,
Frontier: Elite II paper models,etc.