This is the second[0] post I've read this weekend where someone preferred a file-based database system to MySQL. In the other, they explain why MySQL wouldn't be preferable to SQLite in their use case. Here, moving to flat files was faster and easier to work with, at 1/5 the total size, and being much more granular.
They essentially built an ad-hoc database complete with sequential keys and indexing. I'm curious to see what the resulting performance would be if they used a database that's appropriate for the type of data they have. I'm not familiar with non-relational databases but I suspect that a key-value or document store would work very well.
[0] https://news.ycombinator.com/item?id=11934826