Love the game, really nice ideas torcado.
My main gripe is the upgrade selection early on can be a pain since multishot is rather mandatory on several characters, and it seems to evolve very strangely over time with the pool being almost completely saturated with bubble and obliterate.
I can understand not wanting these to appear early, but perhaps an entropy-like system to avoid certain upgrades (and heals!) not appearing for many, many refreshes could make the experience a little smoother.
Your suggestion is essentially what is already happening, Upgrades become less likely to show up in the shop, and are replaced by the action items you see. this is how the game transitions late-game from providing items like health and other upgrades. The intention is that you transition to manifesting those items at that point, since they become expensive enough that they can’t be afforded anyway