What are we up to, ten? I like 10. We should go for 20.
10. The Bridge (or "Command Center") with all the upper echelon officers on duty at the same time, is located on the upper deck of the ship where it's most vulnerable to getting blown to bits along with most of the ship's chain of command. Wouldn't it make more sense to put it in the middle of the hull where it's safest?
This is as much a policy problem as a design flaw. The ship's CO, XO, 3rd, 4th and 5th in command should never all be on duty in the same highly vulnerable area, especially during combat. And if they weren't in the starring roles of a poorly written space opera, they wouldn't be.
You just knew I'd de-lurk to poke fun at Trek, didn't you? Well, now you do!