Vince Young was easily the best player of his era. When left to play the game his way (that's a deliberately loaded qualifier), he could not be stopped. He may have spread the ball around to keep his teammates interested, but outrunning the entire defense was always an option.
After that, I'm looking at a couple of QBs known for their decision making skills. Colt McCoy could throw just far enough and run just fast enough to make the plays Texas needed. He could fire the ball within his abilities through the tightest windows because he knew that was where the play should go. I still maintain, though, that he was out on his feet when his pass hit the crowd railing with 0:01 on the clock. Sheer luck.
James Street mastered the "new" wishbone offense. This was the unstoppable offense that would break college football. Wherever the defense went, the wishbone powered the other way. No defense could possibly stop four runners, plus deal with the occasional deep pass as well.
I admit this is recency bias. I just don't know enough about Bobby Layne. Also, I'm sure there are tons more without the glowing trophies. Peter Gardere's undefeated streak against OU should garner him a mention.
I believe Sam Ehlinger's abilities were not maximized by Texas. Between lacking proper OL play, competent QB development, and an OC without imagination or foresight, he had better skills than he was able to show.