Bo probably isn't the GOAT of all college QB's in history. Different circumstance factor into all the other stories, different philosophies, different rules, different opponents makes this a very subjective rating and I'm sure there are valid arguments against Bo being THE ONE.
BUT ... there is not another QB in the country I'd push him aside for this year. The Best in the conference is the best in the country. So why does Bo get the top spot in my eyes. Part of the reason is my love of Oregon football, which is not enough to win the argument hands down. There are other reasons. His competition is probably playing for USC or Washington. They are strong candidates but fall short.
Part of the reason Bo is better is the offensive line and his use of it, each making the other successful. Neither of his competitors has that going for them. Bo has been sacked, I believe, four times in the first nine games and at least one of those is his falling short of a gain by about a yard. There have not been bunches of full face meetings with defensive players with blood in their eyes. He doesn't have to panic often. Actually, I'm not sure he ever does. He knows when to get out of Dodge and does it under control. His sees his check downs or the sidelines while progressing through his reads and doesn't make the wild throws the other two do, sometimes successfully. Those last resort plays make highlight reel material, but not good strategies.
He runs as well as either of the others but doesn't do it more than is prudent, and when he does his carries are usually successful. I think he learned his lesson last season, or the coaches did. The scouts from the next level are not impressed by a QB featured as a runner, It won't be part of the program for whoever drafts one of them. I don't doubt them admiring his ability but am fairly sure they admire his restraint more. Penix seems to like to do the same thing but is forced do take off more often, a choice dictated by the unwanted company he has in the backfield. Williams is on the wrong side of the plan and is also at the mercy of the other teams in decision making.
He can make all of the throws but doesn't make the haymaker his weapon of choice thanks to a strong running game, something he can only hope play with in the NFL. His superlative completion rate, pushing 80% even with the drops all QB's face, is significantly better than the other choices. I'm a bit too lazy to hunt down the comparisons but I believe he leads the nation in that and is the all-time Oregon best. Most of his throws don't wind up in the hands of teams not wearing uniforms that match his. Both Penix and Williams fall short and have to make a lot of the long throws and they do it well. More often than he, they throw to wrong team or at least throw passes which can be intercepted. They also fumble, he doesn't.
Most of all, he is unflappable. His record number of starts have given him experience and the confidence he has. Perhaps, the start of the Cal game in the rain is the best example. Starting with a first and 15 followed soon after by an interception of a well thrown pass, muffed possibly because the ball was wet, to a player who would later be the leading receiver of the game, might have shaken younger less experienced young men. Not only did he shake it off and continue executing the game plan but he showed his receiver he still had confidence in him. He didn't turn to his leading receiver much because the defense was already doing so. Still, he found him from time to time, once in the end zone as the clock wound down on the first half.
Bo most consistently runs the machine without turning the ball over. He leads the machine efficiently, quickly when he needs to, eating up clock when that is the plan. I see him as an NFL guy playing against college teams. Always under control, even in the Washington game where clearly outplayed Penix and put Oregon into position to send the game into overtime, in an away game. On another alien turf where almost all other good teams fall to Utah, he made the game so one sided there was no crowd effect by half time. In fact, the only game Bo has lost aside from the trip to Seattle, while healthy for the entire game, was his first, against national champion Georgia on the east coast.
We can't know what Penix and Williams would do with advantage of the team and his coaches Nix plays with, but it is unimaginable they would be better. I'll stick with the known over the maybe.