I feel that trade runs made to resolve crises, while good for small amounts of reputation, should provide experience similar to how experience is rewarded on pirates. Enough to make it worthwhile to trade, as otherwise you're simply running goods back and forth and making a bunch of money, but your character never improves.
Also, perhaps it's only my games, but I started a new one due to getting tired of the bounty hunters sending craft after me, despite being positive rep with them (in the 500 range), and almost immediately the Omni were set upon by both the Starborn and the Empire. Currently, they are down to three planets, after roughly an hour of play time on this character, with the Starborn taking four and the Empire taking two. I know there's supposed to be a dynamic world and all, but something affecting the game world that quickly really should be kept in check. And I haven't even joined a faction yet, so they should be on equal footing.
I've never actually succeeded in one of the escort missions either. Usually the merchant simply runs off at the first sight of pirates, and books it to the jump he was originally at, or makes it to the planet, without another word. Any idea how those are actually completed?
Regarding balance between some of the classes of ships: The Typhoon II, a gunnery focused frigate, has the same energy core and regeneration as comparable missile or drone frigates, despite having two medium turrets and a small, and two small missile slots to compensate. Little pieces of balance like that I hope are smoothed out in the long run, as it otherwise is a fairly large drawback to take for little benefit other than harder hitting main guns (and lots of cooldown time when waiting for them to recharge between shots wipes out half your energy bar).
Another random idea, brought on by one of the random chatters from another pilot, is to have the wormholes shift, as this could dynamically change trade routes, making easy routes more difficult, or opening up new, more lucrative routes with ease.
I've noticed a few spelling and grammar errors here and there as well. One that specifically comes to mind is Hatsya, which states "[...] is ideal for crops & wilflife production," and another for Talon's perk tree that describes the "Firely upgrade" (presumably the Firefly upgrade).
Weird bug I've noticed from time to time using the Predator MIRV missiles, is that occasionally it'll spew out a plasma variant missile rather than a normal kinetic one. This seems to happen when both MIRVs are launched with the 4 key, and they explode at the same time, but also results in one of them not actually producing any missiles.