I think adding feedback for marking cells as dependant on each other might be a good idea.

I'd also love code completion in notebooks.

I think the cleaning and code reuse problems can easily be mitigated by putting functions into libraries and using auto reload.

My normal workflow is hack something in a notebook until it runs, then refactor and put in a library I import with auto reload. I work on production ML and I use this for both software development and research.