First files went into a hot folder for color conversion based on the paper type to be printed on. This took care of spot color separations, RGB imagery, L*a*b* color definitions, et cetera. Then we ran everything through a little Acrobat Preflight that ensured that the fonts were embedded and that forced all white elements to knockout.
PitStop's new version has some tools that will make checking margins a do-able thing.
To check document size(s) (never correct) would require a zillion preflight profiles. I'm hoping that Adobe and/or PitStop will put together a preflight pathway that would bring up a dialogue to input certain parameters - like page size, page count, separations, et cetera.