I like sqlite as much as the next guy but it's built-in datatypes are limited. Things like arrays, UUIDs, geometry stuff, JSON, etc. Sure you can store more advanced stuff as blobs or text but then you have to mess around with deserializing it in the host language and you lose the ability to query it directly in the db engine.

Also the moment you need two databases for high availability or access to it over the network you end up inventing mysql but using sqlite rather than innodb.