Hi there,
I will address it as it had some of your points and hope for further constructive feedback.
For the debugger overlay, we did land a pref that allows you to switch it off (devtools.debugger.features.overlay) and will expose it in UI later as well. We had positive feedback on the feature itself, as compared to other tools, Firefox's paused state was very subtle and could have gone unnoticed. We will surely collect more feedback on the overlay and improve upon it to make it less obtrusive while solving the aforementioned problem.
Removing Scratchpad is not an easy decision, as it has some strong advocates. We did interview many of them and pulled their feedback into Console's new multi-line editor mode. This also helps to bring the benefits of Scratchpad to a broader audience in one of our most-used panels. We will continue moving use cases from Scratchpad, like load/save or onload-execution, over to the editor mode based on user feedback.
Regards,
/Harald