Yet another reason to wait a while before diving into Beth games is for the respective wiki to get properly compiled. There's a whole lot of stuff that the game doesn't explain, and while reddit has been a wealth of information, it's a lot easier to have a wiki that'll provide you with detailed stats and whatnot. I suppose the stats are another thing that'll have to wait for the CK to be released.
I got the Mantis ship last night (awful quest, BTW, too many trial and error bits), and then discovered a whole nuther area of shipbuilding that I actually do have access to, so pretty much scrapped it save for a few parts I wouldn't otherwise be able to afford.
Another issue I'm running into is storage space. After a quest or two I can have 10k+ credits worth of discarded weapons, but no way to actually get them to somebody to sell. Moreover, I'm trying to stockpile resources on the off chance that I actually do get to craft some stuff, and that's also a PITA.
As for balancing, IIRC FOV had a perk (or several) that allowed you to get bonus XP, or perhaps more perk points. Something like that would help here. It's not like you can just focus entirely on research and crafting while ignoring the necessities, so building a complete character will take a ridiculous amount of time. Shitty game to be a polymath in.