okay lets go from top down
1) your lasers have little to no firing arc
2) your supply to the laser/eb module is trash and you dont have enough energy in that module
3) your missiles have a very bad supply and you are wasting hella money on production
4) your supply for energy to ions is also trash and you also dont have enough energy
5) terrible supply for EMP to launchers as well as oversupply and not enough energy
6) why do you have a whole small reactor dedicated to only 12 standard thrusters
7) nukes have wayy too much nukes and not near close enough launchers
8) tb doesnt have enough power and has bad supply
9) use engine rooms and make larger reactors rather than spamming smalls for thrust
10) holy shit your cannons are so explody and i really want to chain them
11) why do you have missiles down there and also they have very bad supply and not enough launchers
12) on the bottom of the ship you did well by adding engine rooms and using the single large reactor but its very exposed from the back
13) crew! alot of your places are either under or overcrewed and that is either wasteful of money or wasteful on effficiency
now for some things i love about your build,
1) the shape, its such a cool shape and really want to fight this thing being scared of it
2) the idea! the idea of a ship with ions in the middle and missiles on the side with cannons on the wings is super cool