ProtoExpo Ok. Ships like yours need smoother and simpler shapes, as they do not have the space for crazy shapes. Now I'm not saying they need to be bland bricks, but still. Also, there are too many modules, thus making it explosive. If you do need modular parts (like the ion prism), separate the modules as bigger, more all-round chunks then specific areas and having multiple. Lets take what I said and apply it to your ship (just as an example)
The engines have too many modules and crew. To fix this, beef up the thinnest parts of the engines (like the connection point) from 2 to 4 (no triangle armor doesn't count). next, spread the reactors to the center of the engines (so that way if you launch the fighter enemy missiles don't get free reactor shots when they curve.) Also, you can basically cut the crew down from 24 to 18, since having 7 thrusters only require 6-8 crew. Shields need to have the bare minimum of 4 but can also have 6. Weapons only need 1 crew quarters and 2 bunks to work (with crew manning the guns). There needs to be more pd, and more armor around the engines.