I was asking this same question myself when I first started out using Prosper202 to track my PPC campaigns. Fortunately, this question has already been answered on the Prosper202 forum.
Prosper202 will provide way more data than Google Conversion tool and will also support several other traffic sources where as Google Conversion tool will support Google Adwords. It will also consolidate data from multiple accounts into one interface, track searched query keywords as opposed to just bidded keywords, and allow subids tracking and postback url tracking where as Google Conversion does only pixel which Prosper also supports. In short, there are several other features that Prosper includes that is not in Google Conversion tool.
You can read the forum thread here.