From what I can gather of the design process, the 3.5e rules (and 4e rules) are part of the minification of D&D. The 3e rules are basically a DM judgement call. The 3.5e rules (and 4e rules) provide a fast* and consistent way of determining whether a creature has cover or not when playing with miniatures. I think they succeed in their aim pretty well, although my more casual players have terrible trouble with the ranged cover rules. (They think "from centre", not "from corner of square").
(*well, it's meant to be fast)