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1. Academic code. Not one institution would pass the Joel Test[1]. You pretty much covered some key points in your first paragraph, so I see not much has changed. The best predictor of how something will perform in the future is how it has performed in the past. Just hiring good software engineers won't change the system in which they work.
2. Academic bureaucracy & administration. I've worked for large Fortune 500 companies with less byzantine org charts. I've been matrix-managed. The siloing in academia is crazy.
3. Advancement. Because it's academia, advanced degrees are everything. My first boss in academia had a PhD. His job? He ran the student computing lab. My second boss was an MD/PhD. Great guy, but treated everyone like a lab assistant. I went to graduate school for one year and realized it wasn't for me.
4. (added after reading other comments). Completely unrealistic understanding of what developing robust, complex software is like. You touched on this by mentioning how many projects have 1 maintainer. I remember seeing a doctor shopping around his project plan. I'd say it would be a challenge for a high-performing 5-person team. He thought it was a job for a single entry-level programmer.
1 https://www.joelonsoftware.com/2000/08/09/the-joel-test-12-s...