I think the other thing at play (other than losing out more at JUCO talent) is that the offenses in the Big 12 in 96-03 are not the offenses that emerged once leach really came around into his own around 2005 and on. I think that not only did Bill have more talent in the late 90's/early 2000's, but the game was also a slower, more plodding game, and coming up with big home run places put you at an advantage. The roles are almost reversed today. We are really the only team in the Big 12 that purposefully tries to slow down the game, take as much time off the clock and reduce possessions, and of course play as clean a game as possible with the least amount of turnovers.
Sure, a significant part of that is due to not having as much top flight talent, but it also conveniently suits our lesser amounts of talent, and makes us once again the "odd ball" team out of the bunch, which I think makes it harder for teams to prepare against, and since we see basically the same thing from every team, we don't have to alter as much in prepping for them.
As for Nicname saying if this development has hurt us more or not, I think really all it's done lower the ceiling and raise the floor. WE won't ever be super amazing I think under this plan, but we won't fall off the map either.