Damage rules. 'Sins' ships are binary in one way (perfectly functioning, or destroyed), and weirdly organic in another (given time, they repair fully at no cost, no matter how damaged). No dead crew, no irreplaceable parts, no ammunition limits apparently. It would be interesting if there were derelicts essentially created by killing all the crew on board a ship; one could see possible research or intelligence benefits should one be able to board and thoroughly examine, in addition to the obvious salvage.
Logistics rules. Supply/ammunition modeling is fairly limited. Missiles, armor, et al should impose physical requirements. Maintenance should depend on actual ships in play and how much wear/tear they're on.
Economy. Option for finite resources meaning asteroids *run out*, thus adding impetus for expansion. Option for planets themselves to provide resources.
Order queueing: when queueing up multiple builds, don't charge for a build or upgrade until it's actually started. If it can't be paid for when it's supposed to start, pause it until it can be.
Standing orders. For fleets, designating a fleet's area of operations in which it will move to engage known enemy fleets (i.e. "if idle, and enemy fleet known in <any of certain marked areas> engage; return to post when done". In general, targeting preferences and 'auto-join fleet' prefeferences.
If we really want to be fancy, some research upgrades probably shouldn't be applied en masse for free. In other words, fleets and structures might need time/resources for the necessary refits. In such a case, it would be near-obligatory to reduce micromanagement by having a mass-retrofit cost and an 'automatically retrofit when applicable' toggle. This, combined with better damage/ordnance models, would help replicate one of the interesting aspects of space conquest as per some science fiction: if you're the aggressor, and your fleets have traveled far from home, not only do you need to conserve resources because your supply lines are long or non-existent but your target's technology may have had many years to advance during the time your fleet was in transit. Some things, like better programs for your computers, might be simple to implement, but if it's an entirely new type of armor or a new propulsion system, for instance, that shouldn't be instant and free.