I had a 05 2500. Was a good truck. Replaced water pump once and front end once (ball joints, tie rods, u joints, etc). Front wheel bearings were a frequent issue, but they are on most vehicles today. Rear ujoints once. Dash was fine, I live in WI though. Body was starting to get some small rust bubbles under the paint.
I traded it in because I wanted new and didnt need a 2500 diesel anymore and I hate rust. It got a heck of alot better mpg towing than my 18 Ecoboost does towing.
I wouldnt be afraid of a well taken care of 3rd gen, as long as it didnt come from the rust belt.
Oh in 06 they changed the interior a little. I liked the 03-05 better. Some years have tow/haul, some years have OD lock out, some years have both. Unless your towing REAL heavy, I dont see a need for OD lock out.