Yeah seems like it would _have_ to be storage related but my profiling tools are limited. I've run Doom on this same processor/flash combo and loading assets from the WAD files is on the order of 1ms and I can run Doom smoothly at 70fps. Not very scientific but that's part of the reason I was surprised by how slow SQLite is running.

I wonder if it could be doing multiple small writes on every operation -- I could definitely imagine small writes getting very costly, especially with wear-leveled file systems that might be moving around pages on even small writes.