Items :-Atropos are to weak compared to Reapers, both have unlimited ammo. The RoF is higher but their compared damage takes render them close to useless ( or Reapers to high )
-Antimatter Blaster : Damage compared to other weapons to low , while fluxcost is high compared ( if it should be considered a better emp weapons ... i think it is not)
-Heavy Mauler : Same as Antimatter Blaster
-Ion Cannon : I think this weapon is somewhat OP in your mod due to the "shield piercing effect" or makes it a must have weapon ( 1 or 2 makes most of the enemy ships helpless )
-Guardian PD System : RoF lower than its ammo regen.
-Heavy Blaster : very low flux compared to the damage
-Many ammo based weapons needs more ammo , the often run dry to early in bigger battles ( even with expanded magazines )
Ships :- Onslaught Built-In Weapons : RoF to low , fires way slower then the ammo regenerates.
- Paragon : Only fought 1 yet , but I think that in player hands its invincible , hard flux dropped while using Fortress Shield. Killed it only because he dropped his shield instead of using fortress shield again .
Shipsystem :- High Energy Focus : Minor "bug" when active it shops -75% damage in green while it should show it in red. I really didn´t notice that debuff at first in the heat of the battle.
Skill :- Navigation : Very strong
but some eg. Level 1 and 2 stats are the same , I think 10 it was ( for captial ships ) the jump is to high , would be better if it increased to that number over some levels.