Your idea was to create all star systems (normal terrain) close to each other on one map (map1), surrounded and therefore seperated from each other by impenetrable terrain (ocean). But you can leave the star systems (map1) via gates and start star trekking (map2 - normal spacetravel, not hyperspace) in order to travel from one system to the other. Quasispace should be an own map, including invisible railroad tracks and only available to a restricted number of vessels, the flagship, Arilou, Orz. Colony ships are OK, but maybe shouldn't be able to leave their home star systems. Great ideas.
Hyper- and quasispace maps should only have tight tunnels connecting the systems, increasing the chance of encounters there.
Some star systems should also contain ressources or Melnorm traders or even lifeforms (all units with 0 defending capability and no chance to leave the system) that give you credits or special techs.
A tech tree is hard to integrate in this game, it will alter the StarCon2 concept completely. Maybe you can slightly change the image of your upgraded flagship when you get better cannons (Leonardo's?) or another idea: exchange the normal fleet ship to be produced in less time (with less ressources).
Wouldn't it be better to give all minor races to the barbarians? So each system would produce only their native ship type? And if you conquer/destroy their capital planet/unit, you'll get the necessary tech to produce that ship. (Event: the capital planet reappears and belongs to the attacker-civ, meaning a race's system can switch sides several times if another civ destroys that unit). If the units are classified as attacking units, the AI won't pay a lot of attention on placing piles of units inside the cities to defend them, only a single one. All the others would roam in space.
And the major races should be civs able to gain a better ship later in the game (e.g. Chmmr & Chenjesu, Humans, UrQuan) or simply modified and bigger drawn unit images including weapon fire.
Another idea would be to classify your flagship as a helicopter unit, which constantly loose hit points if there is no starbase/city. This means you could travel a lot without outposts, but the chance of getting a critical hit would rise, too. So you need friendly cities in outer space to keep the ship in good condition for attacking other civs.