neither XML, JSON nor zip solve the problems SQLite does, though; if you use plain old files, you need to make sure any changes you make actually end up on the disk, consistently. This is not easy to do. It also solves any consistency issues that might stem from someone reading the data while you're writing it.
On top of being just better, having a relational model for your data gives you much more freedom to use said data; you'll be able to do things efficiently that might require restructuring your JSON or XML format. Personally, I love SQLite-based application formats because I can explore them with SQL, which is often much easier than trying to make sense of a custom JSON or XML schema.