My ideas
Make so that missiles do not bypass shield, but increase their damage a bit , maybe make them do same damage to shields and hull.I guess you tried to make something like rockets and mines in FTL? but in FTL you have very limited amount of rockets and you cant just spam them so:
Lets add blue slot "torpedo bay"
Lets say it costs 500 scrap and you have 5 charges, to use it you must select enemy and click on Torpedo icon
After you used 5 torpedoes slot torpedo bay just disappears and you have to buy new one, or you can sell your current and buy new one, selling torpedo bay gives you 75% cost for each torpedo, so if you have 1 left you will get 75 scrap in return
Torpedoes have good HP and homing as missiles but has move speed of unupgraded nuke. You can use it across the map but because it will behave as current missile, enemy fighters can "catch" it or just shoot it down, so it would be nice limited "firepower boost" and maybe limit of 1 or 2 slots per ship, or maybe increase its cost , the more you want to install the more it will cost , so you cant just spam them, or maybe make cost of 1000 scrap so it will cost you alot to spam torpedoes.And because you have to buy slot in order to recharge it you cant do it in combat, so if enemy destroyed all torpedoes - "gg noob, learn to clean path for torpedo" , i guess it will balance things.
Second idea - Science vessel
You can buy science vessel to fly with you, it has yellow triangle slot and very few blue slots for self defense
Into yellow slot you can install 3 modules 1) Bay research 2) Defense research 3) Offence research
When you install it , every, lets say, 3 turn you get random buff or new weapon for this category you can buy and install into your ship, without any special visits to stations , just with scrap (as in original Battlestation)
