Anonymoose (Guess someone should let you know there's an 'edit' function when clicking on those three dots appearing in the lower right corner of your reply when having the mouse above it. Wouldn't want a mod to mistaken that as post farming...)
Say, you ever had a look as some building guides in the guide section? If not, you should have a look at them, they provide quite some useful knowledge.
Now, about your ship:
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the lowest shields, the outer flak and the inwards facing ion beams have no doors
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most modules would work just as fine with about half the reactors they currently have (exceptions are the ion arrays)
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use energy storage only when knowing you will need more energy over rather short periods of time or close to the hull, where you wouldn't want to place explosive reactors.
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the ship lacks side- and frontfacing thrusters for maneuvering
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crew bunks only provide two crewmembers on the space crew quarters provide three, meaning you should use quarters rather than bunks (unless you really won't need more crew, as additional crew (1000 credits each) costs more than the bunk/quarters difference (a total of 250 credits and a 1x2 space))
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the entire frontal center section lacks shields and/or armor
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quite some prisms aren't linked and therefore don't fire
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armor is quite heavy and slows your ship down, only use it to protect things, not to fill empty spaces (your armor interlacing is pretty good btw)
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engine rooms are rather expensive, try to fit as many thrusters as possible on the same engine room to cut costs and don't fill every available spot with thrusters, as that reduces stability and simply looks unprofessional
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you'd usually want as many weapons as possible shooting the enemy at once, that's why the cannons on the sides are rather unbeneficial
(Still working on a ship for you to fight against.)
