The download version added higher resolution and widescreen support.
However, due to multiple issue with code backups, some of the changes in the later disk version patches were lost. Mainly, Finnigan is not a good trader and will not sell you back his magic lockpicks if you complete the quest to retrieve them, and the lockpicks will disappear if dropped directly on the ground (not that you'd ever want to drop them), and a couple of rare bugs are slightly less rare, and probably a couple of other things I don't recall specifically.
Resurrected creatures die in the download version, rather than turn hostile, when the character gets too far away, so that can not be used to farm XP or loot.