* the big one for me: very limited migration support, requiring quite a lot of ceremony for common tasks (eg rewriting a whole table and swapping it out)
I don't know where this idea of having to swap a whole table in SQLite came from, but it simply isn't true. Over the last 13 years I have upgraded production HashBackup databases at customer sites a total of 35 times without rewriting and swapping out tables by using the ALTER statement, just like other databases:
https://www.sqlite.org/lang_altertable.html
For the most recent upgrade, I upgraded to strict tables, which I could also have done without a rebuild/swap. I chose to do a rebuild/swap this one time because I wanted to reorder some columns. Why? Because columns stored with default or null values don't have row space allocated if the column is at the end of the row.