3.5 made all 3.0 material (functionally) obsolete. Some stuff could be run with tweaks (modules and monsters mostly) but PC crunch all had to be revised (Hello Complete Warrior, goodbye Sword & Fist) converted by hand, or discarded. Most of the DMs I knew did the first or the last. Many (myself included) didn't allow 3.0 crunch after 3.5's arrival. Even as a DM, I rarely used MM2 because of compatibility headaches.
Pathfinder is the same, but worse. It will change the underpinnings of the game enough to make most crunch obsolete, and the nature of WotC's OGL means much of the crunch produced by them cannot be revised. It leaves two options. Convert or discard.
That is the crux of the matter. Some DMs will be content to convert and capable of doing so. Some will do it well, others will do it poorly. I think many more will be content to discard. It further aggrivated by the notion there will be plenty of fresh 3.5-era crunch (Third Age, Dungeonaday) that isn't Pathfindered. (For good or ill, once 3.5 hit, all 3pp converted to 3.5 to jump on WotC's bandwagon. I don't foresee the same universal acceptance of Pathfinder, though I may be wrong).
Thus, Pathfinder stops looking like a "revision of the 3.5 ruleset" and more like "a new RPG based on the 3.5 ruleset", really no different than Trued20 or Castles & Crusades. I think at that point Pathfinder should have been more honest with itself and really fixed the problems of 3e (something more akin to SAGA in looks) and ditch the notion of "backwards compatible" OR pretty much done a few nip/tucks on glaring 3.5 problems (polymorph, natural spell, sneak attack) and reprinted the SRD pretty much as is. (Which was the original goal: keeping the 3.5 rules in print).
Because by being beholden to two masters (innovation & compatibility) you compromise the best of both.