I'm surprised that you have files that really should be going in the user's personal folders?
If it's application related run-time data on a per-user basis, that's what appdata is for (which is broken down per user, and restricted/roaming). I would argue that BF2 does it wrongly, if it is storing anything there other than files *generated by the user*.
But updates of BF2 or your software are not user-generated files... those are your companies files, and they don't belong in the users _personal_ folders.
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So to be clear, if you're saving a Word document, or a saved game, those belong in the user's Documents folder (possibly - Word shouldn't be in a special folder within documents, and there is a specific folder dedicated to saved games which nobody seems to have noticed).
But configuration data and application cache data or any other data that needs to be written per-user but is not really something anyone but a power-user should ever directly manipulate should be in appdata\ someplace.