The biggest issue for new players is the fleet management. It's hard to eyeball how a particular ship in shop will do without trying it out first. Same goes for weapons. I'd say the missions in main menu almost feel like a tutorial after the actual tutorial, unless you're a fan of reloading saves in campaign. And the best/worst thing is the autofit. I can see the use for new players but how can he/she know that the autofit build is actually doing something in combat. To me autofit just seems like something you use when you have multiple of the same ships or just wanna put literally any weapon on a clunker ship. If I were a new player, I'd rather experiment with everything so I don't get the ''I obviously need more ships'' feel some new players get when they use bad builds and fleet comps.
Speaking as a noob with about, I don't know I ain't got Steam to count it for me here, maybe 50 hours in this game although you are right that it is virtually impossible for a new player to know how a particular ship could or should perform looking at in the shop (I still can't do that, I rely completely on watching them in the field) I don't think this is the biggest issue for learning how to play.
I think there are two bigger ones which are very much related:
1. The flux/overload/shield/armour system and the resultant necessity (usually) for cat and mouse combat. I am not aware of any previous game that uses a system like this and any new player is most likely to be completely stumped as to why they are getting their arses handed to them to begin with ("begin with" equating to three or four times more play time than the average AAA action title takes to complete). It's not just complicated, it's totally unfamiliar.
2. The plethora of confusing weapon types and variants. Many games have a rock, paper, scissors model which is usually quite simple and familiar, but this one is more like (rock, paper, whatever)^2 except that a rock looks like a sheet of paper, the paper is scrunched up to look like a rock and whatever is just, well, whatever. The new player has no hope whatever of understanding what all these weapons do and how they should be used, certainly not until they've played for three or four times as long as the average AAA title etc. But the real kicker is the way these weapon specs interact with the flux/overload/shield/armour system. That's were the ^2 comes from.
Not that I'm in any way complaining, it's what makes this game great, sets it apart, but IMHO if something quite imaginative is not done to ease understanding of all this stuff when it gets released on Steam it is not difficult to imagine the cacophonous whining and avalanches of -ve reviews that will ensue.
Dark Souls may have been difficult, but the principle behind it, monsters having specific attack patterns you had to avoid and specific weaknesses you had to to exploit is hardly new or unique. You could argue that that's all that's really going on here but the difference is in Dark Souls you are just trying to whack your foe with a sword, not rocket science, whereas here it's much more complicated or certainly seems to be to the new player.