I mean as cheesey as Jedi Rocks may be, I think the CG Sy Snoodles is heads and shoulders above the rod puppet they used before, and things like putting Ian in Empire really helps everything gel for me (not just gel with the prequels but gel with ROTJ first and foremost)
That said, some of the things they did in the 2004 DVD are not quite as good to me, such as the lack of musical fanfare when Luke goes into the trench on the Death Star, and other audio issues like that (Leia and Tarkin's patchy VO's when he's about to blow up Alderaan), stuff like that, but to me, the improvements of the 2004 SE outweigh any of the issues it has introduced.
When it comes to people saying the sabers aren't all colored right, I have to say that it was pretty dicey to begin with in the classic trilogy, especially in ANH with the experimentation with the reflective rods and such.
I guess the way I see the 2004 SE is it's better than the O-OT, but it's still not finished and I roll with the fact it's not yet finished, just as I rolled along with the monkey woman emperor in ESB. One thing that's great about the 2004 release, is now he has input from all of us rabid fans who notice every little detail. No person in charge of continuity for any given film can compete with the millions of fans like us when it comes to being anal retentive.
And I say anal retentive in a good way. It just means we care more and notice more.
I think it's great to be so observant, but at some point we have to keep in mind that it will never be perfect, and if we want to get the most enjoyment out of these films, we have to work with them to a certain extent.