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From what I understood, there are two reasons. First, the literal, in that you really DID have to kill Tchort because, like a jerkface, he was boguarding the computer that controlled the southern elevator. And, even though you're technically part of the Institute at that point, Tchort probably caught wind that you were (willingly or otherwise) working for Six and was therefore not going to trust you.
Secondly, Six wanted Tchort dead because Six is one of the Godmen and, as I understood it, Tchort already ate one of them and intended to eat the other two in order to become powerful enough to make it to the surface. All Tchort ever wanted was to see the sun shine .
Congratulations on making it through. As far as story goes, Deep Caverns is probably confusing and disappointing to those who go in without having found certain bits of lore in their playthrough. But even with those, many mysteries and uncertainties still remain. Expedition won't continue the cube storyline, but it should shed some light into other mysteries.
If you don't mind spoilers, buried somewhere in the forums there's a nice lore discussion thread with a misleading title: http://underrail.com/forums/index.php?topic=2260
Regarding the general suggestions, I like most of those. But why do you want to change vigorous belt? Just seems oddly specific. And it's a godsend as it is, for early levels on high difficulties with low con / psi characters. You can loot corpse piles of any size if you empty them completely, that makes them non-interactive and lets you click on the next one. There is a vendor who sells all kinds of fish, but he's so rare that crafting some drugs demands you to do your own fishing.
The levelup system is one of Underrail's peculiarities that I'm pretty sure Styg won't change. It was done differently from Fallout for a reason - to prevent players from metagaming the system and taking only high level perks and/or abusing temporary stat boosts to unlock them. Having to spend all skill points at once also changes the nature of the skill system a little bit, since you can't save points to suddenly go from 0 to 100 when you find a skillcheck for that.I was my first run and I didnt knew where to go and which skills should I take. I was hoping for more flexibility giving this suggestion.