I do not know who would be the most intelligent but I would thing that the more people that can identify with what you are rapping about would put you up the scale.
I'd say Mr. Lif is the most intelligent rapper out there http://www.mrlif.com/, http://www.adultswim.com/williams/music/defswim/mp3s/08_Lif_red-october-clean.mp3 lyrically at least. As far as who is the most intelligent academically, thats anyones guess. Some rappers have degrees, so I'd say there are some highly intelligent artists out there. However most rappers, even the ones who go to college, don't complete school if they are actually successful in the music business. Why would you rush to get a degree if you are getting rich selling music?
Tupac was of average intelligence I'd say, but he was extremely talented. I think he was a better actor than Will Smith, and would have been like an Al Pacino if he had stayed alive, but he also hung out with the wrong crowd, and all the talent in the world wont help you if you have bad ass gangster friends. I respect what Tupac was trying to do, but if he were really the most intelligent rapper of all time he'd still be alive.