Pre-finished: advantages are faster and easier installation, minimal disruption to your home, fast cleanup time and usually less expensive labor costs because sanding, staining and coating are performed in the factory. Also, you usually get an extended warranty with prefinished flooring, and finish that is very scratch resistant.
Unfinished: Advantages are availability of more wood species, widths and cuts that can be matched to existing wood floors. Also, unfinished flooring allows for custom onsite sanding, staining and coating with a protective sealant after installation to achieve a beautiful unique floor.