The game needs variety, more sense of difference between the factions and more tactical problems on the map.
1) Scouting is crude and poorly handled. It is just stupid that space-faring species are unaware whether there is a gas giant in a system. However, when other factions would want to oppose a scout, there is no problem- a scout sees everything in a gravwell on entry. Sentient beings hide when damaged. Hiding is fun! Clouds, storms, asteroid belts, all should reduce scanner ranges, as should dark sides and inhibitor devices. Ambushes are the heart of RTS.
2) There is too little variation in terrain. Planets of the same type are exactly the same size, why not randomise this slightly? Phase jumps are equally quick from any gravwell, perhaps differentiate by type? Lets have more part-blocked gravwells, space swamps. Also, in the original game, the stock pirates need a phase inhibitor or two to be effective as a block...
3)As a simple means of introducing variety, how about a single-stage upgrade for weapons and speed for each researchable ship type, so that the basic level is lower than it is currently?
4)The early defences are too weak, very early rushing can kill the game. Make basic defences drastically less expensive, as it is they are incredibly overpriced compared to ships. This affects new players especially.
5)Specialisms- more complex trade and government as well as diplomacy and pirates. How about three different flavours of each faction- monarchy/oligarchy/republic- and a special ship to research where you have to choose one option of three specialist ships for the rest of the game, perhaps either cloak, marines(ramming/salvage) or destroyer(heavy cruiser hunter)- effectively that would be nine factions.... The cloak and marine ships could just be slightly altered versions of existing models, it would help with their abilities.
6) Implement team bonuses, how about slightly faster research when an ally has already teched it? Also, why is there no xenophobia? Teams of more than one faction should need to research intercultural competence to be effective.
7) Its a ship game, they are about trade and convoys, not just strongpoints and mining. Bring the trade and refinery ships into the game more, have them produced at the factories, set individual routes for them, abandon the current crude and silly method for calculating trade.
8) More abilities and counters and counter-counters- if players want perfect balance they can play as the same faction. A greater range of tactical options and variation of terrain is much better for gameplay.