I would like to see in patch 2.0
The ability to build a shipyard anywhere in space with use of a constructor.
The shipyard by default must build small ships only.
The shipyard must be upgraded using constructors to allow anyone to build bigger ships.
The ship yard must be upgradable to allow faster repair rates to ships (also upgrades to the shipyard must have defences and weapons to allow the shipyard to defend its self).
The shipyard should be allowed asteroids bonus to allow it to increase its shipyard production rate.
For economy buildings a unique building to increase the output like the manufacturing buildings get a bonus from the fusion plants.
Allow starbases to be built around the planets and allow the defence of planets
Allow ships to be added to starbases using logistic points and of the ships to take part in base defence.
The spy system needs a good improvement.
I personally liked the spy system galciv2 and would like to see some elements like just spending money to get some general intelligence and would like to have such a system in place to be able to spend money on limited defence to stop spies from spying on me as well as get some level of intelligence on other races.
I would like the system spend money on limited intelligence of other races and spy defences to be integrated with spies to do more advance stuff like kill of enemy spies or my spies be given orders like steal a spaceship or technology, Destroy a building or starbases, help cause a planet to revolt or with enough spies influence a government to ally with me or go to war with me, use spies to reach the highest level of intelligence of other races (used in conjunction with spending just money on general intelligence on other races).