Excellent game
I could buy a game that looked somehow like that on Steam, but the difficulty of the game kept me away. When I saw yours I thought it was the same concept and I almost decided to stay away from it, but since I like this kind of game (when they are easy to understand), I gave it a shot.
Good points:
+I love how the guns just shoot by themselves, all you have to do is move around.
+You don't have to shield particular part of your ship, the shield covers it 100% always.
+Allies act by themselves unless asked otherwise.
+Building ship gives almost infinite possiblities.
Bad points:
-You can only have one tractor beam... Either add a part that can add more of them or make it we can tractor as many items as we want. I lost loot because I couldn't carry it around.
-Infinite space on the ship... While it is funny, I ended up with an indestructible battleship that moved super fast, shot around 20 lasers, 3 missiles, 15 cannons plus all the core repairers, energy refreshers and shell repairers needed to support the monster. I could fight in dead sectors easily. You should put a limit on parts you can add until you get the next "ship core level"
-Only one core/ship level. I'd like to see different kind of ships with different kind of base stats and weapon/equipment slot.
-More weapon levels.
-Have regenerating territories and permanent territories... It was very annoying to cross a sector where I had fought a war and supposedly won only to see the enemy is back in there again...
Suggestions:
>Have your own base/territory/factory/whatever you want.
>More allies type and maybe give the player ranks. After a certain rank he could control the stations to produce certain type of allies depending on the situation.
>Stop the random damage in the dead territories. Instead, put debris and what not that if the player hits(make it so they'll have no choice but hit them), they will lose shell and core HP. Just random damage is weird and unimmersive.
>Have new quest like escort the station builder, escort the diplomat(you could add new factions with that idea, but I don't know if it would fit in the story you have in mind).
>Since finding stuff is so easy, maybe make some crafting system where you can melt stuff you find instead of selling it to get some material with which yo ucan build new weapons.
>With the above idea, maybe add a development part of the game where you need to do reasearch! (It would also go well with the idea of having your own base, just a thought.)
>You could also turn this into a huge scale war where systems are not taken via quests, but actually fighting for them and asking for station builders in the havens and stuff... I don't know... This game could grow so big!
Conclusion:
I couldn't think of everything I wanted to put in the good, the bad or the suggestions section, but I think I gave you enoguh stuff to work on for Episode 2 for sure. It was a great game, I played without ever getting bored once(well, not until I had my invincible battleship with spammed equipments). It still could grow into something even more amzing given the time and the help from others probably. If you are good enough, I could see this as an indie game you could download for free(or for a price, if you are really that greedy) on the internet. Keep up the good work and you get a 10/5 from me!