I would like to second Steve Litt's plea for a well-formed Lyx native
format. I wrote a script to create a package to submit to a journal from
my paper's Lyx file. The package includes a tex file with the
bibliography and figure files renamed with standardized names such as
fig1.eps. It makes copies of the re-named figure files in a subdirectory.
As it stands now, the code will break if I upgrade from my current
version of Lyx. If there were a well formed native format, my script
could be written once and used with new versions. I could distribute it
to Lyx users who need to do this common task.
This is just one example of the Lyx add-ons that Steve envisions.