"What is slow are the arbitrarily complex index interactions that come with the relational world. "
Index's are arbitrary if arbitrary created. It has no bearing on the relational world, no more than a bad driver makes all cars bad.
"Given the example above I think SQLite could be a great implementation leveraging the power of stored procedures to implement atomic datasets."
1, SQLite doesn't support SPs (You can use C to write extensions however) and 2, I've got over 10 years experience in RDBMS and I've never heard of an atomic dataset. Has anyone else? I struggle to understand how a set can be atomic.
"Using BerkleyDB or Innostore could remove the slowness and pain of interacting with the data through SQL."
This kind of comment needs to be addressed. There is NO pain in using SQL, the pain that is perceived is the lack of understanding and skill to use it on the part of the user. Don't call something painful simply because you haven't taken the time to understand it.