I am a spread option proponent in real life, although I had to give it up in NCAA in lieu of a similar offense to what you're running because I hate the lack of plays in the spread option scheme.
Starting in the shotgun 5 yards behind the line of scrimmage is WHY the spread option is so successful. The two downfalls of under center option attacks are that it is difficult to get north and south and it is difficult to throw the football. Being in the Shotgun or Pistol allows the option to attack down hill, forcing the defense to make a decision quickly. Under center, outside options can be strung out indefinitely with a disciplined defense.
Where under center gets its strength and what made those Nebraska teams so successful was that roughly 70% of their runs were actually not option. They ran traps, pitches, powers, designed belly gives to the FB to help set up the outside option you're talking about (you'll see that some this year with 2011 Nebraska). Shotgun spread option offenses really can't install those types of plays outside of a few teams who commit to it 100% (Oregon, Florida under Meyer).
These comparisons are why the Pistol has taken college ball by storm lately. You get the strengths of both worlds without sacrificing much of anything.
I personally prefer lining up in the shotgun (outside of this game) because in the end, most QB's are more comfortable with the reads from the gun and you can open up the offense a lot more than say a Paul Johnson can at GT (Paul Johnson himself calls his offense a spread offense). If I want to run a three back option offense, I can do it with the QB 4-5 yards behind center just as well as the Flexbone or Wishbone using any number of formations. There are some things that just work better out of under center, like the trap and belly game, but they are replaceable by things out of the gun.