Optimizing SQLite is tricky. Bulk-insert performance of a C application can vary from 85 inserts per second to over 96,000 inserts per second!
Background:
The answer to your question is that the newer SQLite 3 has improved performance, use that.
This answer Why is SQLAlchemy insert with sqlite 25 times slower than using sqlite3 directly? by SqlAlchemy Orm Author has 100k inserts in 0.5 sec, and I have seen similar results with python-sqlite and SqlAlchemy. Which leads me to believe that performance has improved with SQLite 3.