"I want a filesystem in a single file. I'll pick the one I'm most comfortable with and pretend that it's much better than separate files". Meanwhile, we'll ignore all the semantic issues around the data. What exactly _is_ a layer? Any given image file? What if some tools only handle e.g. alpha-layers? What if a layer is actually a filter kernel? How are the layers composited? How are they ordered? Is it a linear orde…
That way, you could standardize on the semantics that are already documented and familiar to other developers, but avoid the difficulties of the file format, which seem to be the issue here.
* disclaimer: I've never had to write a PSD-parser, I'm just going on hearsay.