support ships is a very general category. if we are talking strictly of "support ships" as things that aren't really supposed to have a place in battle, my complaint is mostly that they don't EVER take part in battle. while adding any kind of ability to attack them without first confronting every single gunship the enemy has first.
i hope at least that long-term we will get some sort of simulation of supply limitations (for the AI, anyway- we have lots of limitations already) ideally the finished game will have the ability to actually wage a more constructive (destructive?) war against various factions and actually debilitate / conquer them. a critical part of that will probably be raids / logistics attacks. ideally i'd like to have "endgame fleet" mean more than "has the biggest and heaviest ships available" i guess. personally i think it should be possible to take apart an enemy fleet without necessarily just lining up your gunline and shooting them to pieces at standoff ranges. a bunch of phase raiders are strategically extraordinarily lethal (in theory..)
but how this stuff should (ideally) work out just depends on how far alex wants to go with actually putting in actual war. i think personally if i had to choose a bunch of features for 1.0 top of my list would be:
real production (IE, empires do not just spawn infinite ships)
real logistics (IE, fleet outposts have a finite amount of supplies to supply their AOR and if those supplies are destroyed en route then you can actually weaken the fleets there)
convoys (IE, actually escorted transports that mean something if destroyed)
deployment rework (IE, the ability to deploy enemy ships and to have your ships deployed, the ability to shape the field and deploy things in different places depending on certain factors, the ability to somewhat control battlefield terrain, etc)
battle rework (making it more phase / terrain control based where you can't just "deploy gunline, select autofire, win" putting some strategy and terrain control into it besides just shooting everything to death with no strategy requirement)
sensors rework (more ambiguity in positions of enemy ships, especially at long ranges.. adding of "anti-sensor weapons" that produce false contacts or create uncertainty at medium / long ranges)
i expect that with all this included we can probably have 1.0 in about 10 years :^)