I can only say what I'd do, which definitely might not fit with your vision for the game. But I would reduce the number of chests, so there were only a few per level. Increase what can drop from chests. Make it so that when you open a chest and your inventory is full, the item just sits on the ground where the chest was. Then players can look at the item, and decide if they want to toss something else away to take, or not. That is a fun choice, whereas throwing an item they want away in exchange for an unknown item, its not as fun. The limited inventory is good, especially because you can expand it as an upgrade and that will feel really good.
I didn't notice about the points. But personally, I don't love points as a metric for success. You already have a perfect one: depth. The goal is to go as deep as possible, the chests and items and such are just a tool to help with that goal. The more surprises, challenges, upgrades, etc... you put along their journey the better.