I think the main difference between the DL and WDW versions is the aesthetic (at least from what I can remember, having been on both of them within the past year and a half). WDW's PPF retains that kooky, black-light-painted, look that the true original dark rides have. It brings the look of the ride closer to Mary Blair's wacky color palette, I think. Since DL's PPF was redone with the rest of Fantasyland in 1983, it is actually newer than WDW's and so was made to look a little more "realistic". (You can see this difference right off the bat in the painted backdrops for each ride's load area--anyone have good pictures of them?) So while some would say that DL's is "better" than WDW's for this, I prefer to think that they're just two distinctly different visual takes on the same dark ride--and I'm glad that both are still around to enjoy. I would hate to see the unique WDW version redone to look exactly like its DL counterpart, and vice versa.
That said, yes, WDW's version is in need of a serious re-touching because it is not maintained as well as DL's. So I'm hoping that's what they do with these weeks--cleaning, repainting, oiling things up. Given the short length of this refurb, that's probably the only thing they'll have time to do anyway, and I think that's perfectly fine. No need to change the whole look of the ride, just the condition.