This is a very charming, fresh take on an existing concept.
Here are my criticisms:
The start seemed glitchy. I had one soul but had to go get another just to feed the tree its first one.
The pacing was awkward. Early game I had to do several runs without any upgrades that change how the run goes. Late game I could buy my way through several levels of a newly unlocked artifact.
The first round of artifacts only give you economy bonuses, which at that point don't let you buy anything except economy bonuses.
The Dark Cemetery, for me, performed just a little bit worse than the Enchanted Forest, all game long.
The plant growing aspect was unintuitive, with the plants fruiting then wilting, unharvested, while I wasn't even looking at them. And now that I did figure it out, it seems like it is not useful at all. Even if harvesting always worked, you have to waste valuable time in a run collecting plant seeds.
If holding E to deposit as many souls as possible was explained, I missed it. Holding E to gradually deposit many over time would be more intuitive anyway.
Maybe this is a nitpick but I think the tutorial signs damage the charming atmosphere.