Just some script-related ideas:

1) On puzzles when many scripts are used, it's often a challenge to remember what has or has not been used yet. It might be useful to have an in-game feature that keeps track of recently run scripts in puzzles.

2) Another thing that could be helpful would be some sort of stopwatch, that could be used to determine how long scripts have been running.

3) When a script is running, it would be nice to be able to view the cookbook without interrupting it.