I owned an 03 and now an 05, both 48re auto's. Both very similar equipped- SRW, 2500, QC, 4x4 SLT's so can only compare those two.
You would think my SO 03 would do better on fuel but I have found my 05 does just as well, runs more quiet and comes with 90 more hp.
Both trucks were CAT equipped. Of course being the 03 was an SO, it did not have the added piston cooling the HO's and my 05 does.
My 03 had a separate computer for the trans where later models like my 05 has the engine computer running the trans.
The 03 had smaller exhaust at some points in the system where the 05 has 4" turbo back.
The 03 had an odd TPS, Throttle, cruise control set up that seemed old school compared to the integrated way of my 05.
The 03 had a filter mounted lift pump, mine didn't go bad but the replacement part is now a retro-fit to what the 05 uses.
The 03 came with a 10. 5 rear axle where the 05 uses the 11. 5
The 03 front drive shaft did not have a lube point for the center CV joint at the transfer case like my 05 does.
My 05's Tow/haul function works better IMO than the 03's overdrive/off.
While I would like to choose OD off sometimes while in TH, its just not that much an issue because if I get an unwanted shift to OD while in TH, all that is needed is a double tap of the button and you are there again. Overall shift strategy seems improved on the 05.
My 05 came with a plastic tanked inter-cooler which I don't care for but is still holding together. Blown ones are replaced with metal ones.
Overall I think I like my 05 better and only sold my 03 to give our son a good deal on his first diesel or else I would still be driving the 03.