I can't say that I got to see much of the upgrades system as the game felt very lethal. I would get two upgrades--I think health and damage, since the game was so lethal--then I'd get past that level only to not really have any points for the next level. Additionally I HAD to buy health, because otherwise I'd just die on the next level. So there just was not much to buy.
Retreat/wait/continue seems interesting at an intellectual level but when playing it, I don't think I like it all that much. Part of the fun of a roguelike is exploring the level. This system means you can't explore, you just go forward or backward or stay in the same place. It also took some getting used to. So that's another area where it feels like the decision space is constrained.
Ah I see. Apologies but the game is currently a little unclear here but that the main thing to do is unlock skills on the skill tree. You can do this immediately.
So you didn't interact with the core of the game (a clarity problem I think, which I'm definitely going to patch) and of course it's impossible without doing that. Would love to see you try it again with this knowledge. The part about exploration is definitely true. That's part of Path of Achra, which I'm trying to emulate here.