Hi Draekniloth, sorry you hit that wall. Fixed in v0.5.15: a full Essence Tree no longer locks you out of the Ancestral Sky. The fall takes you to the tree and its heart opens the sky. Your save should work again, tell me if it doesn't.
Your automation ideas are all good ones: a toggle for each automation, letting the auto-buyer skip the either/or nodes, and keeping the auto-trainer from spending gold before skill upgrades. They're on my list.
You're on the credits page too: https://marrowmarch.com/credits/ Thanks!