With respect to limiting runaway production growth. I think the fact that you have to continually spam ships is indicative of a need to rethink how ships are managed.
Games like this are meant to be about thinking strategically.
- What solar systems are most important?
- Where are the key weaknesses in my supply lines?
- In what direction should I expand my empire?
- What are my macro priorities (Population vs Production vs Science)?
- Do I want to have a dense highly developed empire on every solar system, or do I want to have a sparsely developed empire?
For the first 20-40 turns you can do all that by directly controlling units, but as you get past 10-15 developed planets it gets much harder. The fundamental question in my mind is "Why can't I highlight the crucial systems and mark them as such?", "Why can't I highlight a sector of space and automatically settle that space?".
I think long term it would be best to have a fleet management tab where you would select stars and define desired fleet allocations on those stars, and then production would automatically work to fill those targets. Similarly a planets tab which would allow bulk settlement of planets where you could sort by current supply level, planet type, specials would be nice to have. Once you have researched much of the biological and infrastructure technologies planets you initially skipped over because they were hostile are now open to useful settlement, and its a pain to have to build individual colony ships to move them through already inhabited systems to "complete" the settlement of that star.
In the meantime a quick way to bring balance and avoid ship spamming is to have larger colonies automatically divert production for internal purposes. Its rather silly to imagine that a planet with 20 billion people would not have a basic shipyard, would have no defensive fleet, and would fail to settle a habitable planet in the same system. Perhaps as the planets hit various population values they automatically start diverting a percentage of their production to internal purposes. A lot of the decisions with respect to settlement and "defense" of solar systems deep within ones own territory are rather easy, the player just doesn't do them because its a pain to click through 5 dialogs just to get a lighthouse in every system.
If the desire is to not have a ship in every solar system you could instead introduce starbases (think a big slow moving outpost [starlane speed 10, no attack, upgradeable defense, detection/stealth]). Each ship would have to be attached to a starbase, and would refuse to move far from a starbase. Instead of producing individual ships you would instead select which starbase to prioritize, and then within the fleet for that base prioritize the ships stationed at that starbase. When a ship is produced at "Vega" shipyards it automatically travels to the starbase at which point it can be sent out for duty. If a planet was not within the range of a starbase (5 turns) and had a population >5/10 billion it would either become unhappy or start producing its own starbase, to force the player to account for the defense of that portion of the empire. For a mobile attack fleet you could have a flagship, but fleets attached to flagships would not make the locals happy. Expanding the empire then becomes a two stage act:
- Build a flagship and secure the area from threats with a mobile fleet.
- Build a starbase and move it to the desired area (once it is constructed the ships will begin construction), while also potentially relocating other starbases to move favorable locations.