I believe the only difference is in the plastic vs. carbon fiber body work. The 2005 has a different upper fairing ( a little wider, and doesn't have the slits like the '04 has...presumably to cut down on the buffeting but I think it was to satisfy the styling police that criticized the original look of the fairings on the 749/999s).
Also, Ducati North America brought in only 60 or 62 (depending on who you ask) 2004 749s into the U.S. so quantities are highly limited for the '04s. I don't know how many are coming in of the '05s but I'm told that Ducati N.A. will bring in as many '05s that will sell, since the '05 is not a true World Supersport homologation special like the '04 was. From a collector's standpoint then, the 2004 is the rarer bike. I haven't heard anything about the titanium collets on the 2005 though. Regardless, you can't go wrong with either bike! Just get one, change the front sprocket to one less tooth and replace the stock clutch slave cylinder with one from Evoluzione and you'll be all set to go! Have fun!