Has some merit, I'll admit. I thought I liked the idea of having one MySQL database tuned for some of my data and another tuned differently for another lot of data. You're suggesting that flatfiles might be better for some other types of data and perhaps some other, highly custom arrangement better for another sub-domain.
But then, you couldn't do the sort of adhoc stuff on mainframe datasets that we do now on many relational DBs. You had to program something and wait for it to finish. Which might be several minutes, it might be several hours, it might be several days.
I think the role of 'database programmer' is being re-invented.