1 thing. Code review. Even thou notebooks are not meant for production code, it's good to check them into repository to document what you did (let's ignore out of order computation and other horrors), and get feedback on your code / experiment.

Right now, ipython notebook is stored as json, where code is list of json strings (so that you have it line by line).

Additionally, the "WYSIWYG Interface" is horrible in comparison to vim, emacs, idea, pycharm or whatever you are using. What I like about notebooks is being able to present things as experiment: this is the code, and there are the outputs. "WYSIWYG Interface" is good if you want to tweak few things, or if you are starting out.