darkdragon396 It took a while, but I finally managed to have a look at your ship.
The first thing I've got to say is (deep breath to calm down) you've committed way too much armor.
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This thing has more armor than anything else and way too few thrusters for a ship merely half as large and filled with structure instead
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The railguns need better powering, most dual-pd and the rear capital laser turrets too
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A dual shield layer isn't enough to protect the penetration cannons against ships of similar cost. The flak and the nuke launchers aren't shielded good enough neither
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Those clustered pd will hardly protect you from all incoming missiles
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The flak is rather useless, it doesn't target any lasers and any enemy ship will have lots of those
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Not. Enough. Thrust.
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Many energy sources are too far away from the things they're supposed to power
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Too much wasted space
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Use modules or at least actual compartments
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The penetration cannons don't get enough ammo
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Bad distribution of basically everything
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Reactor clumps/lines
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No FE in the upper half of your ship
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Poor door placement
Guess I could go on if I bothered enough, but that's already enough for you to fix.