IIRC, Doug Drexler explained that, they changed the nacelle designs in response to the semi-permanent warping of the space/time continuum established in TNG. The new designs "fixed" that problem so that ships could go back to higher warp factors in the main space lanes without wrecking things. They just couldn't really get there with putting such an innovation on the ships while they were all out fighting the Dominion. Once they stood down from their war footing, new ships built had the new tech and the older ships that remained from the war were upgraded in turn.
That's my head-canon on it anyway, based on Drexler's take, and it's as good an explanation as any to me.