I would like to like YouTrack, but I've always been put off by own custom database [1]. I like my data in relational databases. SQL is the ultimate read-write API. Jira (unintentionally) stands on the shoulders of giants in this regard.
Problem is that DB schemas are unlikely to be exposed as a real API by any app. It may feel like an API but actually writing software that pokes DB tables directly would just create the kind of support and upgrade headaches that presumably are driving Atlassian to this decision.
The other advantage of the JB approach is it's one click install and upgrade. No schema migrations, complicated issues with DBA hoarding permissions etc.
[1] https://github.com/JetBrains/xodus