My vision for Survival Gameplay loop
"Waiting" for research like others have suggested is not fun, nor is it gameplay. Look at how the survival game Rust does research. There are certain special components you cannot manufacture yourself, but must obtain through exploration. I think this could be incorporated into SE in the following way.
1. Do not lock block blueprints, lock component blueprints in the assembler. This can easily be incorporated into your current tiered assembler changes. Late game, when you have T3 assembler, have unique component blueprints be unlocked by attached "Add-on Modules" that you build plugged into the side of the assembler.
2. For certain key blocks like tiered refineries/assemblers and their "Add-on Modules", require a single unique component you cannot initially fabricate. This would require you to explore and find that unique component per block, and once you have built the "Assembler" or a specific "Add-on Module" than you unlock the unique component for fabrication.
3. You can trade off an NPC cargo ship, find a wreck and salvage, or raid an enemy base/cargo ship to steal these components. You could also require a certain tier of Grinder to return the component, and not just scrap metal. Similar to how battery packs work.
4. Part (3.) further stratifies the tech tree and creates emergent missions. Because before you can manufacture a Jump Drive, you need the "Jump Drive Add-on Module" for your assembler, but the module requires a unique "Jump Drive Component" you cannot fabricate yourself. You will have to raid a Dreadnought or Shipyard to acquire one. But to salvage the component from the block, you need a T3 Grinder or else you'll just receive "Scrap Metal" because you botched the removal with your low quality tool. Which means you'll need the minerals, and corresponding "T3 Tools Add-on Module" for your assembler to craft the Grinder (or buy or loot a grinder). But the Dreadnought and Shipyard are not going to just let you steal this component, and they have defenses. Therefor you will need to build an attack craft or find some other engineering solution to bypass said defenses. But be careful not to hit the Jump Drive or "Jump Drive tech add-on module" you're trying to salvage, because you might destroy the very unique uncraftable component which was the entire reason for ambushing this capital ship in the first place!
5. Creating these tiers also stratifies the games economy. More "loot items" with different rarities and values, that you cannot simply just fabricate straight away from raw ore, and require an investment of combat/exploration/materials will create "specialization" between different factions and engineers. This "specialization" will incentivize teamwork, trading, raiding, exploration and looting. (This necessarily requires exploration encounters to be well thought out, designed, and placed in correct locations to facilitate advancement from any starting spawn).
6. Place these encounters and unique components where they will be needed. If you start in space, than have encounters with an orbiter/lander that has an "atmospheric thruster fabrication component", just outside the atmosphere so the engineer can loot it, make the add-on for his assembler, build atmo thrusters, and land on the planet. Then on the planet you can have an encounter with the component that unlocks large hydrogen thrusters, so they can find it, build them, and go back into space. Are you in space and need Large ion thrusters, well search the asteroids for a mining station, or trade ship crossing the void. Need the Jump drive to reach the next planet? Well, the Dreadnought that has the component you'll need to fabricate them lies beyond the moon, just far enough to reach with ion thrusters, but close enough to make it economical to still build the Drive to planet hop.
7. This further increases the fear of loss and survival aspect by requiring you to protect your vulnerable add-on modules or blueprints. If they get destroyed, then you have to explore/trade/combat to acquire another one. This opens up the possibility of LOSING progress, which fits well in a survival setting. It also incentivizes having a base, whether a station or capital ship, where you hoard and reinforce the defenses, of your valuable production capabilities. And since the unique components that give you the ability to fabricate high end components, only affect a single assembler, your production output is directly tied into the exploration, trading, combat gameplay loop. If you want a giant factory of 100 assemblers all pumping out Jump Drive parts, you're going to have to raid 100 Dreadnoughts or trade for 100 "Jump Drive Assembler add-on module components" or w/e you end up calling them. This will give a very rewarding sense of progression and increase in power over time.
8. Increase the # and variety of raw materials, and their locations. I would include Carbons (wood, oil), Gases ( Nitrogen, a Noble gas, Helium), Biological (proteins, amino acids, algae), and more Minerals. And these resources have specific locations. Incorporate them into the new and existing tech tree/blocks/components.
9. I would turn the current Ores, which are just pure minerals, into different ACTUAL ores which are mixtures of different concentrations of minerals. Much like the Better Stone mod does (https://steamcommunity.com/sharedfiles/filedetails/?id=406244471). I would add further gameplay via Metallurgy by making more of the Refinery add-on modules to specifically target certain mineral groups in an ore, like a centrifuge for the more massive minerals (uranium), ferro-magnetic separation, for the magnetic minerals (iron), electro-phoresis add-on for charged materials, acidic washing, etc. Actually put some science, and engineering terms and concepts in for immersion/education. Like a "nano-fabrication add-on module", or "circuit printing module" etc.
Also adding in Heat transfer mechanics to Production/Energy/Weapon/Fuel/Thruster blocks (can be done simply) as well as "Add-on Modules" for mitigating the heats would add further engineering gameplay. Fires in pressurized/atmospheric conditions could damage blocks and adjacent blocks/players.
Radiation (solar, cosmic, and reactor) and shielding (water curtain, lead, magnetic field) mechanics would also add engineering gameplay. Solar and cosmic could affect your health/energy and electrical systems. Maybe it does damage specifically to the "computer" components in blocks. Where reactor radiation may leak and create a slow health draining hazard when they are damaged, creating time pressure in a repair situation.
Finally, increase variety and stratify weapons/defenses. Different types, think Hacking(via communications vulnerabilities like antennae, remote control blocks), EMP, Laser, biological, heat, and ways to mitigate them. That would be cool.