I think the big undo stacks are just the nature of the PuzzleScript medium, like the turning of the pages of a book. Once you've played enough PS games to be "native" they will feel natural. In their simplicity they afford some convenience for the player: hold the button to rapidly unwind the stack; reset from an interesting position to explore some alternative, then unwind through the reset to return to that state; even do so multiple times to maintain a stack of interesting alternative states. Rather like dog-earring pages in a book.