Zachary I think your first submitted ship (that got rejected) has too much things that add cost, but do not improve survivability or firepower (This used to be my problem in the past). Just look at the weapons at the back, they rarely get used or used usefully.
Also, adding a huge cluster of reactors away from the things that need power doesn't improve the energy delivery speed and makes your ship more explody (and costly). Sometimes it is better to have fewer reactors closer to the edge of the ship.
And always, and when I say always I really mean always, try to wrap your shields in armor (I tend to forget this). It increases your ship's survivability by a lot.
And at last, try to compartmentalize your ship, most of the crew is sitting far away from the things they must supply. Put them closer to where they must be, and make sure they only do the part they're supposed to do, and not something at the other side of the ship.
Hope I could help with my own recently accuired knowledge!