The problem Coca-Cola has with Mr. Pibb is that many of their local bottlers have contracts with the Dr Pepper/Seven Up company to bottle and distribute Dr Pepper in a certain region; they will, therefore, not have anything to do with Mr. Pibb.
While Coke can create incentives to get the bottlers to handle Mr. Pibb instead of Dr Pepper, there are apparently antitrust concerns if they were to go beyond that and issue an ultimatum. Many of the bottlers are actually owned by a Coke subsidiary, but they theoretically operate independently and they don't want to appear to be squeezing the little guy out by dropping Dr Pepper (now owned by Cadbury Schweppes, so it's not really that little).
In some places, including Los Angeles, while you can't find Mr. Pibb in bottles, you can sometimes find it in soda fountains that aren't serviced by the local bottler.
The identical situation, by the way, exists with Squirt and Citra: Citra is Coke's imitation of Dr Pepper/Seven Up's Squirt, and it's only available in areas where the Coke bottler doesn't distribute Squirt.