How to store data when SQL sucks

Is SQLite the only option for data storage in a cross-platform desktop app? WTF?

SQL is such a broken leaky abstraction and most NoSQL stuff is even worse (JSON for queries? Seriously?). Either way though none of that helps desktop apps unless you want to manage a separate database process.

I'm tempted to write my own B+tree impl but that's like a pain in the ass. Where is libpersistent-data-structures that I can drop into my project?

SQL is not a "broken leaky abstraction". SQLite is good, just use it. If you hate that and you hate NoSQL, then yes, you need to write your own. You answered your own question.