Problems....
Power Storage - Takes up room, costs, and is useless after the storage is depleted, best off removing it.
Compartmentalization - Force crew to stay in an area by blocking it off, this ensures each section can continue functioning. You'd probably save 500k just on doors and prevent crew running half way across the ship to the next available reactor/ammo factory which hurts efficiency.
Chain reactions - Too many reactors for the ship, means single explosions cause huge damage.
Too Many crew - obvious, very costly.
Both control rooms are right next to chain reacting reactors...seperate them out with sufficient armour to protect them.
Ion Cannons - These are great for constant damage, but you need enough to penetrate shields, i've found anything less than 3 lined up isn't enough to do that, so two together have little effect unless heavily supported.
Can also cut down on the thrusters, think you have at least 100 on there which is overkill, you can overlap thrusters (when you use forwards, you arn't using reverse etc) to save space.
Just a few thoughts on the design.