Ok, I’ll respond to this one at a time.
First, thanks for the typo list, I’ll get to that as soon as possible.
It is because your main stat is agility, pretty much, yeah. The Commander fight is something I know I need to rework a bit- I’ve known that for a while now. One of the things I was going to do was add in an instance where if you do get into a loop and spend too long in the fight, the fight will end automatically and you get the sub-par/bad outcome regardless of preparations.
Short answer, I know it’s a problem, and it’s on the bucket list.
If your relationship with B3 is less than 50%, it will be hostile at the start of the conversation. If it is less than 45% at the end of the conversation, it will confront the protagonist about its aggression.
I think what happened was you had less than 50 at the start, but then did something to raise it a bit, so it was 51% by the end and you didn’t really get they rivalry payoff.
Anyways, yes, its hostility was on purpose.
Thanks! It’s appreciated. 
That’s kind of what I implemented the “Artifact” items for. I’ve never actually mentioned it on the forums, but they do exist. Basically, there are 4 items in the game that, when obtained, boost a corresponding stat by +15. This way you can either make your dominant stat even more amazing, or you can bring up your lower stats so that you might be able to pass more of the checks.
Right now, only the Combat and Charm artifacts are in the game. The Agility artifact is in one of the side missions coming up, and the Intelligence one will be in chapter 7.
Not really. It’s not planned, anyways. He was just a nameless character meant to serve a plot purpose.
Still, I have plans to rewrite some of chapter 2. Maybe I’ll do more with him. 
Ouch. Yeah, that’s a thing.