It looks to me like J.O. is being nudged into the position of fourth big on the team by Chris Wilcox. I don't mind having J.O. in that spot on the roster. Johnson and Stiemsa behind them as 5 and 6 respectively round out a pretty solid big man rotation.
I also think it makes sense to leave J.O. as the starter. Wilcox is more valuable off the bench as he can play both big positions effectively. If all bigs are healthy, I feel fairly confident that Doc will be choosing either Wilcox or Bass to finish games with KG on most nights. The minutes distribution is bound to vacillate between Bass, Wilcox, and O'Neal throughout the season, depending on health, who's playing well at the time, and matchups.
Johnson will continue to get his burn when someone in front of him needs a rest, and I'm sure that will continue to be happening with frequency, including at playoff time.