- Continuously parsing and writing and reparsing text, 90% of which is useless (that's the JSON/S-expressions vs XML argument)

- Forcing a diverse relational structure to fit a tree hierarchy, hand-writing all the logic that manages representation change - either explicitly, at serialization boundary, or implicitly, in every single access operation you're doing to refer to some data;

- Or worse, using an off-the-shelf, generic object/XML mapper, in which case you just compound the bloat even more.

SQLite is one of the single most battle-tested and ubiquitous piece of software in the history of mankind. Anything "simpler" you're going to pick up is much more likely to be buggy and broken, and will definitely be orders of magnitude slower.