Haven't seen a ship quite this big since Project Valkirie... talk about thinking big.
Really good job you've done so far, thou many things require polish, I'm gonna give my 2 cents assuming you want to create something that fits with the vanilla feel.
1. The ship system is ridiculous.... 370 burst speed for a ship this size? No way, Legions and Onslaughts only go to around 330, and they have a fraction of the fire power this thing has. I know you don't want it to be kitted to death but having that mountain of murder sprint at you with the speed of a decked out Hound? That's ridiculous.
I think you should tone the burst speed to around 280-300.
Its regular top speed is also way too fast, at 70 it can outrun cruisers and capitals (while slamming them with bomber salvos time after time).
2. A ship this big needs a lot of range just to avoid being ganked, forget the ITU and go for the Targeting Supercomputer, the bastard is as big as a station so might as well give it the range of one.
Advanced turret gyros also would be a big plus, the more it can use its guns the better.
3. Too few engines given its size, triple the number.
4. Add more guns, the side sections that support the front could easily fit 1 large and multiple mediums/smalls each.
The engine section could fit a few smalls and the carrier sections could easily fit one large and more mediums/smalls.
As far as weapon density goes the side middle sections nail it.
5. Weapon descriptions are lame, a better description for the Super Mjolnir would be "Born from the same hubris that created the Atena, the Super Mjolnir (I'd call it the heavy mjolnir, but whatever) boasts improved flux efficiency coupled with a heavier shell and extra gun barrel. Such a heavy and specialized construction render it exclusive to the Atena, as any other vessel would require a major redesign to implement."
6. The super pd weapon looks ugly and is pointless. if you're afraid of fighter spam just add/repurpose several medium slots with dual flak cannons. Flak cannons love fighters.
7. This thing should have high maintenance and hardened subsystems on it, also the fuel consumption and crew requirements should be increased. Its logistical demand needs to reflect its power, especially once you have campaign integration.
Well thats all I can think of right now, you are on the right track, the ship looks gorgeous already and its potential is big.