Most sophisticated and intelligent musician

Peter Gabriel
Frank Zappa
Van Morrison
Brian Wilson
Peter Asher
Booker T Jones
Jon Leventhal
Bob Dylan
Donald Fagen
Robert Fripp
Paul Simon
David Byrne
Thom Yorke

David Gilmour, Al Dimeola, Neil Pert, Tony Levin, Agree with Knopfler, Clapton,maybe you should have narrowed it by instrument. Names just keep popping in my head.

Bill Bruford, Stan Kenton, Emerson/Lake/Palmer, Stanley Clark, Bela Fleck

Lyrically, Beck's stuff on Odeley was sick smart. I'd also add Paul Simon and Tom Waits for lyrics. Theo, props on Gilmour for his beautiful phrasing on guitar...he hits licks and subtleties that one cannot imagine being played any other way.

I interpreted the post as asking about traits of the person, not of their music.

So I did not include intelligent musicians that do not come across as sophisticated in general as people, even if I might think their music is sophisticated as a result of their intelligence .