2. No obvious way to make your colony have decent fleets.
What do you mean as "decent"?
Basically, if you have a playthrough focused on the "yellow" skillset, you will be in for lots of pain as constant expeditions defeat your fleets unless you are babysitting them with your own custom fleet.
I am managing to do such playthough right now, but only because I put my best colony on same system as a core world, while having a comission with the faction there, thus whenever I get attacked that faction that defeats the attackers instead, but it is obvious no matter how strong my colony gets (it already has all military related buildings maximum, including with the pristine nanoforge) it will never get strong enough to defend itself.
For example: Hegemony decided to attack my colony, despite having the high command and fleet strength of 370%, Hegemony still outnumbered my fleets by 3 times, and had much more capital ships than I had, only reason it wasn't an well... Onslaught, was because the faction I work for interfered, and split Hegemony fleets, each hegemony fleet stopped to fight a different allied fleet, and only the weakest fleet, that had instead of Onslaughts, lots of freighters as biggest ships, that reached the station, and fought it, even then although the invasion was "defeated", overall Hegemony won, they left the system while still having almost all capital ships alive.
If you want to play as trader instead... well, doesn't work either. The previous economy each market would pick some other markets as trade partners, thus trade routes were possible if the trade was indirect enough, for example if the flow of goods was: miners on left of map, refineries on middle, factories on right, and pirates defeated the refineries, ore would overflow on the left side of map, and factories would have shortages on the right side, you could them make a buck travelling all over hauling things.
New economy is always "global", for example Askonia and their crazy fuel production, you will never have fuel shortage enough to make people pay through the nose for fuel, unless you bomb Askonia or something, so if you are playing as pure trader you are screwed.
Even enemy factions right now trade with each other freely, the "access" value is weirdly, global, for example if you are hated by everyone, your access is low, if loved by everyone, your access is high, but if half of factions hate you, and the other half love you, the access is the average, thing is, those that hate or love you, will pay the exact same for your goods, so for example fuel again: enemies of Sindrian Diktat, can still buy cheap fuel from Askonia, even if they are personally sieging Askonia, because unless everyone hates the Diktat, the "access" of Askonia will never drop low enough to make fuel expensive.