I meant to delete the first sentence (and did now), sorry. It’s probably hard to  be the first.
My more controversial / situation specific things:

Personally, I tend to copy code into one giant notebook and I think most configuration things (argparse etc) are terrible.
When you have all your stuff in def main(): and I change something and get an exception, I cannot use ipython -i foo.py to inspect the variables in main.

But these are really me.