Did some digging. The most prolific QBS that were a part of E11 since its inception in 1999 are listed below:
*I'm labeling QBS "prolific" based on any one or combo of:
-Heisman
-Natty
-Top ten draft pick
-10+ starts in NFL
1999: Matt Cassell
2000: Matt Leinart, Kyle Orton, Derek Anderson, Kellen Clemens
2001: Vince Young, Drew Stanton, Troy Smith, Trent Edwards
2002: Chris Leak, Jamarcus Russell
2003: NONE
2004: Mark Sanchez
2005: Josh Freeman, Jake Locker, Tim Tebow, Matt Stafford
2006: Tyrod Taylor
2007: Blaine Gabbert, Andrew Luck, EJ Manuel, *Mike Glennon
*will have 10+ starts this season barring injury
2008: Geno Smith
2009: NONE
2010: Teddy Bridgewater, *Cody Kessler
*Currently has 8 starts
2011: Jameis Winston
2012: Jared Goff
2013: Deshaun Watson
No need to go any further. There's still guys in 2011 class that haven't been drafted yet.