After a long time of thinking about this, I finally decided to drop SQLite as the main database for my Action RPG engine. After a couple years of work on this project, I realized I couldn't work anymore with databases unless I had a good ORM to back it up. And honestly, it didn't seem worth the effort.
By using JSON serialization to handle the game project save data and configurations, we can now have a much cleaner data structure, that will also allow for easier customization in the future.
Since one of my main intentions with this engine is to work with local schools by offering game developing classes to kids, I think that this stuff should be as simple as it can get.
So JSON it is.