I would agree most strongly with number 6. Having spent time in the biotech arena, there are so many fractured data format structures. A good example of this would be small variations in .fastq files. There are different formats generated from different equipment, and different software expects format A when you have format B, and I've seen people trying to shove the wrong formats into pipelines that blow up or create a tone of work as a result.

Honestly though, the biggest problem with people using python for bid data though is just the opposite of number 2, sometimes you need to use that framework, but when you rely too heavily on various frameworks, that's how you end up in dependency hell, largely due to the aforementioned format issues. eg. Framework 1 update fixes bug X but creats bug y in framework 2's parsing.