Note: I did not read through every post and topic, so these ideas may have already been proposed and, of course, these are opinions based on my experiences. What I state as fact could be inaccurate as I am not an expert and have not studied the game meticulously.

I really like Reassembly. There are spaceship customizing and building games already out there, but Reassembly's ability to make a ship from almost complete scratch is fantastic. That is Reassembly's strong point, but, after doing nothing but building a ship from a Command Block over and over again, it gets old. With recent updates and beta features, after a long time of being bored with reassembly, I'm excited about it again! However, when I try to play Reassembly, it is still uninteresting to build a new fleet. So here are some ideas I think will help treat this problem:

Resources: when you kill a ship, it drops Resources, plants will drop R after a while, and certain blocks can generate it. There is enough R created that it is ensured the AI will not run out of resources to build more ships. I don't like this. If one of my faction's stations are destroyed, I won't care since me and the faction can just spawn at another station. If a station is building a 300 P ship when it has 20.000 P, it doesn't matter since R is such a common currency that I can go grab another 4.000 and tell the station to build a bigger ship. Resources should have value, without it, my ships don't have value. I think (when respawning) it should take an equal amount of credits as the P value your ship builds to, and resource drops from every source should be significantly lowered.

Map Generation: a large randomly generated map enables every faction to come into play and a "new" experience every time. I don't think that's necessary. If not every faction appears right at the start, then value is given to a map. Since Africa has low industrial development and little natural water sources, the areas with rivers and lakes are more valuable than those without. Likewise, Siberia has lots of natural resources, but the freezing cold and big, ancient forests make development difficult. So European Russia is much more populated. (Limited faction and resource spawning would also make wormholes more important) Randomly generated is also not required. If a creator could make a custom map, then it would enable custom challenges and (if bunch of other features were added) stories.

Scenarios and AI: Currently, factions have different attitudes and will either: attack on sight, wait until you attack first, or flee unless you're an easy kill. This is always the case and player decision making revolve around how do I build this ship or do I try to kill this thing. Faction relationships and attitude alteration would make the game more alive. These 2 factions hate each other, you destroy ships from a faction, one approves and gives you a better opinion score while the other disapproves and lowers your friendship rating. With a high enough friendship rating, a faction won't try to kill you or your faction, perhaps help you out when fighting someone, or even unlock that faction! Another way to add onto this would be Missions. A faction puts a bounty on an agent/capital-ship/station/factory, booleaning the bounty (EntityAlive: false) grants resources, credits, approval from the faction, and maybe unlock extra features. (like a new block or perhaps alter/spawn a faction!) Missions could also enable story lines as completing certain missions could unlock new missions. (and of course text would be added as mission descriptions)

Combat Mechanics: There are some things I noticed about combat that I think could be changed to offer a smoother experience. When an AI shoots at a enemy, it burst fires (unless it's point blank) and is very picky about when to fire. Why do that when you could spray and still have maximum energy? The AI also doesn't begin shooting until it knows it's going to hit instead of when they enter firing range. A player could damage a ship as soon as it enters range but the AI waits. This shouldn't be since you can regenerate the energy as the enemy gets closer even if you miss. I'm thinking that the AI queries whether it has enough energy generation, and then switches firing mode from aim and shoot to I'm a 7 year old, so kinda aim and then spray.

Customization: I've used the Reassembly Web Development Kit, it is extremely handy for creating mods. I've used the sandbox, it is not handy for creating mods. Making the sandbox closer to the in-game editor would be nice, but what I think would be even more handy, is putting the RWDK into the sandbox. I think being able to customize a block without having to exit the game would make modding much smoother. Make some blocks, make a ship, tweak the blocks, make more ships. Doing this is taxing when you have to open and close the game every step, and would be even worse without RWDK.

I'd love if you found this useful.
Sincerely, the guy who sounds like his Grandpa when he preaches.