All I can say for sure is that they were never intended to be different. The 2005 refresh was supposed to unify the aesthetics of the Premium DT Beyers, as well as introduce the three different impedance versions of each (not to mention it was the introduction of the DT880 Pro). It was not supposed to modify the sound signature. That said, I've read opinions all over the map over which one, if any, is better. The main theme was that the differences, if they exist at all, are slight. HeadRoom claims that the upper bass and lower mids on the 2005 version were filled in a little more over the 2003 version. I've come across a thread somewhere on here that more of less agreed with that. I've also read reports that the treble might have been toned down slightly in the 2005 version. I seem to remember one member absolutely hating the 2005 version, saying it sounded smoothed over and bloated, but his experience seems to be far outside the norm. Either he got a bum unit, or else he was just very sensitive to whatever was different between the 2005 unit he tried and his personal 2003 unit (we can't discount that his own 2003 pair was somehow significantly different from the others of its vintage, after all).
I've noticed that the earlier version doesn't come up as often. The 2005 version must have sold far more units--given that it has a huge advantage in production duration, that probably makes sense.