Prefinished floors will get you material that has been factory finished using very high end machines. They are likely to last much longer. However, choice of colours and type of finish is restricted to what is available. A few manufacturer's do allow you to customize your requirement, but there are limits to this. It is diffcult to repair or redo pre-finished hardwood floors.
Unfinished hardwood floors allow you to decide on the sort of finish that you want, though they do require a fair bit of expertise to acheive uniform finsihes. It is much easier to repair or redo an unfinished floor, becasue you are aware of the combination that has gone into the finish, in the firsr place.