Ok, a couple of things here.....
Firstly, I discovered something about the flagships in general here.... up to this point I'd been only using the Thoraxian ship, since it's the one I randomly started with. Thusly, I'd been basing all of my opinions about the mechanics as approached by that one ship.
When I tried out some of the others..... ugh. Honestly, I cant tolerate it. They're all just WAY TOO SLOW. Frankly I'd thought the Thoraxians werent very fast, but it turns out they ARE the fast ones. The others are so slow as to be painful. ALL of them. If even the Thoraxians were that slow, I'd be going for the "skip all battles" thing as soon as that was implemented. I dont tolerate "slow" very well, really.
Even with the game speed multiplied (above 2), they still move like a brick in sludge. It's also utterly impossible to avoid things when moving like said brick, which is absolutely necessary on the higher difficulties, particularly as enemy range increases.... you cant just tank everything there (and you cant defend as much now with less abilities available VS weapons). But they cant avoid pretty much anything. And dealing with situations where there's nothing in your immediate area and you need to move accross the battlefield to get to other targets is torture. Yeah, I know about the speed-up buttons, but honestly, if I have to use those just to put up with the fighting at all, there's something wrong. Ideally I shouldnt need those at all.
So that right now is the big one for me. Others are likely to disagree, but.... there it is.
The Thoraxian ship is what's keeping me invested in the combat.... without it, I'd not be wanting to do it. I'll be sticking with only that one for now.
Secondly, the weapons. An option to use the mouse wheel to switch between them would be wonderful here. Trying to do it with the number keys, considering the high frequency of switching, just gives me hand cramps. Granted part of it is that my arm is acting up a bit, but still, it'd be a very nice control option to have.
The new weapon mechanics overall are pretty neat, I like these.
Third, and this is another big one: There's nowhere to get BP.
I think probably 99% of all of the BP I'd used in my previous game (restarted now because of changes) all game from ship destruction..... but they hardly give you any now, and of course to get it that way a mission of that type needs to A: exist, and B: have alot of ships in it. I actually dont think I can test any further with this build, because there appears to be literally nothing to do. The only friendly missions that ever appear are the pirate ones (which of course only happens if there ARE pirates at the time), and those dont give BP. And were I stuck with one of the slow flagships, nearly all of it would have to be pumped into repairs as it is anyway, due to them being forced to tank most attacks (again, not playing on Normal here). You can get free repairs from some missions, but when you're dealing with other things (particularly assassination attempts) is when that bit could be an issue.
I'll mess with it a bit more, but I'm pretty sure I cannot go any further at this point.