Admittedly... I have to agree the complexity is verging on being problematic. I did need quite of bit time to understand every of the more intricate mechanics (combat/flux, CR/fleet management, trade/intel), and that was while I had the time to master one before the next was introduced. I can imagine having to learn all of them at once being overwhelming.
But since Starsector is, as you said, great because it is complex, better presentation seems the only way to go here. I'm sure Alex is aware of it, since he's constantly working on it. To know what has to be done is not to know how exactly it has to be done though, and the real difficulty lies there.
Mh...
I tend to agree that the heap of numbers is terrible for ship comparison. Though, I'm not sure that any UI could even remotely compare to simulator/fight experience with the ships. Combat is just way to multi-faceted and context dependent. So... give up on being comprehensive. The only way I can think of to really make this more approachable, is to reduce the UI complexity so much it becomes downright misleading. That is, give ships a few classification numbers and hide everything else behind a "more info" click. Like this:
Tempest:
Combat rating: 8
Logistic rating: 4
Burn speed: 6
Tarsus:
Combat rating: 2
Logistic rating: 7
Burn speed: 4
(1-10 could be the vanilla range, with potential for mods to be rated higher/lower. Maybe also include crew/freight/fuel.)
I think it is OK when a number is somewhat misleading/oversimplifying (which is has to be when the ratings are auto-generated), as long as the game is honest about it and doesn't claim/imply perfection.
I also had the idea of tutorial courses within the game, offered on certain markets, that you can enroll in. So, for example, you enroll in a trade school and get all the trade related tutorial pop-ups. Or you find a smuggling tutorial on a pirate station. Same with fleet management and later features. That way you would not be spammed with tutorials that you presently don't care for, and you could repeat them at an time. In this context the game could also go more into the underlying principles, like that the trade is event based, not routine based.