If I may, I'd expand on the whole upgrades thing. I think straight upgrades would be bad and take away from the designing challenges and the fun of trying to out-engineer your opponents. Instead I suggest "sidegrades".
Playing the game, you would earn points one way or another (although at the moment it could simply be points for each ship destroyed). Then, you would have a screen with icons for each option. At first they would be locked, and after unlocking them, you could activate and deactivate each option for each individual ship. Maybe include a painter tool to switch things on many ships at one time.
Now, for the actual "sidegrades":
1. Volley: standard cannons shoot twice as fast. Does not apply to Large cannons. (So it actually doubles the ammo consumption, too.)
2. Agility: lose maximum speed/acceleration in exchange for increased rotation speed.
3. Conservative: Energy weapons/shields consume power cells at only 1/3 of the rate, but reactors produce cells at 1/2 the rate. (makes ships very energy efficient, but extra vulnerable to electro-bolt type weapons and other sudden increases in need for power cells)
4. Paranoid: All crew carries fire extinguishers, but their speed is limited to 3/4 of its original maximum.
5. Reinforced: All non-armor blocks have slightly higher penetration resistance, fire resistance and 20% more HP, but are 20% more massive and 25% more expensive.
6. Alloys: Armor blocks are 50% lighter, but twice as expensive.
7. Heavy Plating: Armor blocks are 50% tougher, but twice as expensive. Multiplies cost if combined with Alloys.
8. Power Convergence: Reactors produce power cells twice as fast, but can only hold two cells at a time. (could be a block, to be honest)
9. Crowded: Bunks and quarters can hold twice the crew, but their speed is limited to 3/4 of its original maximum. Penalty multiplies with Paranoid (Speed reduced to 56,25%, not including reductions or boosts given by walkways)
10.Supercharged: Thrusters provide 20% more thrust, but consume power cells at a rate of 1 per 2 minutes. (Value to be tweaked, may not seem like much, but it adds up quickly)
11.FTL Optimization: Increases FTL Drives coverage for efficiency purposes, but increases jump fuel required by 10%. Charging the FTL drive costs 50% less power cells. (Values to be determined, basically makes placement easier if you find it hard to achieve >90% efficiency at the cost of "maximum" efficiency.)
12.Extra Consoles: Slightly increased sensor range as long a control room is crewed and operational. Multiple control rooms stack the bonus. Control rooms consume power cells 20% faster and cost 25% more.
13.Precision Strikes: Missiles are more agile (thus more accurate) and can take an extra hit from point defense before being destroyed. Missile factories operate at 66% of their base speed.
14.Artillery: Cannon shells have 50% more range, travel 25% faster and deal twice the damage, but fire twice as slow. Ammo factories operate at 33% of their base speed (due to reduced fire rate). Combines with Volley as expected (major ammo drain, though.)
15.Streamlined Coils: lasers and electro-bolts now fire in a continuous beam with perfect accuracy and no travel time. Requires an additional crew to operate each.
16.Phase Modulation: Shields are 50% stronger, but now require a crew member to operate them.
17.Insulation: All modules (including shields) are now 50% resistant to electro-bolt power drain. All modules consume power 33% faster. Stacks with other effects that increase power consumption.
18.Inertia Dampener: Nullifies any rotation and movement caused by weapon impacts but reduces acceleration (and thus braking, too) by 15%.
19.High-Tech Suits: Crew can now pass through fire without taking damage and moves 20% faster, but costs twice as much.
20.Junker: Reduces all module costs by 50% (except armor) and lowers all module HPs by 50% (except armor). Does not affect crew hiring prices, only the modules themselves. Combines with Reinforced additively so modules have -30% HP, -25% cost and slightly increased penetration and fire resistance. (Bonus: Gives the ship a damaged look? As if it had taken 50% damage? That'd be hilarious!)
That's about all the ideas I have with the current content! Enjoy!