Having played this when it first came out, I think adding the craft-button and auto-craft system are both major improvements to an already amazing game (both in gameplay and graphics, plus sound design etc).
Might be just me, but while I like the new auto-craft system, I think it could be optimised by removing the need for having the item, or at the very least, not making it stack when someone gets another of said item. I think as well, auto-crafting could be extended such as instead of needing to craft a book then crafting a specific mutation: the latter step is removed/done automatically.
Other than that caveat, congrats on the amazing game!