I think you have too many guns interfering with good design.
First off, you don't have enough ammo factories to run your cannons. You need 3 factories per 4 cannons. Also, only the two cannons closest to the factory can possibly fire at full speed because there's a crew size bottleneck preventing cannons from efficiently bringing ammo from farther than 4 corridor tiles (2 room tiles) away. Keep an adequate supply of factories very close to your cannons or they just waste space and manpower.
Second, you don't have corridors. Crew move far faster through corridors than through traversable components. It's okay to have to go through a few tiles of bedroom to get to infrequently used components like point defense or sometimes engines, but you usually want nothing but corridors between a gun and its ammo or energy source,
Third, your second version has its FTL clumped. You'd only need two if they were in the wings.
Fourth, your internal engines are inefficient. Try to get more overlapping exclusion tiles by putting them opposite each other or using a rectangle of engines. As little armor as you have making them internal isn't doing you much good anyways and they're taking up space that could be corridors.
The corridors are the most important problem to fix, the others are just costing you money and wasting space making it more difficult to fit in adequate corridors.
