This is a really cool and creative concept! I do think it's a bit complex, so I would only give this to the more mechanically minded members of my play group. The idea of tracking which stage you're on, which benefit you've chosen, and changing that every respite seems like it would be a lot of added mental work to me. I could see myself getting used to one benefit, then forgetting I had switched off it at the next stage.
I love the names of all the benefits. "The Looming Quiet" sounds sick as hell, and works well with the mechanics.
I don't think that all the benefits of these stages necessarily have to be balanced, but it does strike me as a bit odd that some are just strictly worse than others. Like spring's "budding talent" vs autumn's "a change in color." To get a skill in autumn, you have to drop another skill and it's only in the same skill group? Sounds kind of steep. Especially when other benefits just give you static bonuses that will have huge impacts on combat.
Overall I really like the flavor, and the concept of cyclical boons is really interesting. I could see other versions themed around lawful clockwork beings, or the four elements, or phases of the moon or something.