In the Crux Multiverse they had a function where you found Precursor artifacts that could be used to upgrade ships. It was rudimentary at best but was one of the few things i thought was an improvement to the game.
I honestly liked that part of SC:III back when I played it but always wondered if the Precursors had obtained a method of seeing the future to seed that area with upgrade items for various races.
I believe instead of finding a single magical artifact that'll upgrade ships near instantly, how about an event based R&D upgrade path.
For Example:
Step 1) Locate an artifact of unknown use & origin randomly or via a quest. -- Note this artifact could be on/around a planet/asteroid/sun
Step 2) Take it to your base & offload it for the R&D lab to research it
Step 3) Event happens after X time period stating a breakthrough had been made, but essentially it was incomplete and incompatible with our current tech requiring repeat of steps 1&2 a set number of times. Upon completion of device...
Step 4) Notification that the device from above could benefit 1 or more known race ships, or Starbases, but would require every ship in Fleet X to be rebuilt with said tech to utilize it for massive upgrade items & Starbases would take Y period of time.
Step 4a) In the event of the device not directly helping any species/fleet/starbase the commander would state "We have a fully functioning X but have no clue how to use it or for who to use it" upon finding the right Species needed, after a period of time the commander would start a new event stating the R&D team dusted off "spilled coffee on" the device and realized it would work for said new species.
Now this could work for the ships if they're modular and/or open up new parts for custom ships at a certain point in time.
Possible upgrades
Weapons:
Damage Output
Accuracy
Firing Distance
Energy Consumption
Engines:
Thrust output
Fuel Consumption
Energy output to the rest of the ship
Hull:
Strength
Allowed size(s)
Increased efficiency in energy transfer from engine/reactor to devices
Etc
the list could go on & on.
Edit: I believe possibly each completed research could effect different ships in different ways. Say R&D Project 1 upon completion would increase the speed/range of the Human's Missiles, where as for Race 2 it would increase their ship turn rate, and Race 3 would get a minor thrust increase from it.