I agree that the whole warp speed thing needed to be rethought, along with the idea that there really were huge distances between the Enterprise, DS9, etc. and home base. They should have established that DS9 was so far out that even at "maximum warp" they were still a good year away from Earth, rather than them being seen shuttling back and forth between DS9 and Earth as easily as between DS9 and Bajor. Not to say all the earth episodes were bad, but they did serve to undermine the "Deep Space" premise a bit.
This especially started falling apart when TNG attempted to establish a warp speed limit. Remember the S7 episode where it was revealed that warp speed was hurting some race of aliens, so Starfleet put in a Warp 5 maximum (or something like that) -- and how this was almost immediately ignored in TNG except for I think one episode, as well as DS9 and VOY? The only long-term effect was that the writers no longer specified "warp factor 9" etc. and instead introduced the term "maximum warp" as a catch-all. Certainly subsequent episodes of the 3 shows and later films never seemed to suggest that the "speed limit" was causing any sort of inconvenience. (BTW odds are Starfleet's brain trust probably figured out a workaround, but there was never anything mentioned on screen to suggest the speed limit was ever lifted.)
Cheers!
Alex