Your top priority should be getting art. Even art that looks like you modified George's sprites in MSPaint. Using the vanilla art without modification for functionally incompatible weapons and ammo factories is not good. It is most important that rooms be identifiable in blueprint mode and least in the external view. The icons on the weapon/defense control rooms just interfere with the paint scheme, they don't serve any useful purpose.
Speaking of the control rooms, they're problematic. Having everything gated behind them makes the early game completely vanilla and having them so large makes the early game longer. If they were 2x2 (based on the cockpit since you don't seem to be able to sprite from scratch) they'd be much more placeable on a tier 2-3 budget.
I haven't tried a science design yet, but while a single component is easier to build around in symmetry mode it won't be usable in upgrading existing ships because it's so huge.
