Way too many people seem to need 60+ seconds to select a beverage, select a flavor, add ice and fill their cup.
Second, the flavors are a granular additive. The flavor tends to be off due to poor mixing, the age of the additive, or cross-contamination from the previous user. More on that below.
Third, they're high maintenance. Which means they're usually in poor condition at fast food restaurants. The last one I interacted with was out of almost all flavorings and almost half of the beverage options.
I love the options though. You can only rarely find a place that carry Creme Sodas, Mellow Yellow and the other 'fringe' beverage options that just are not available on a standard four, six or even eight nozzle dispenser.
Edit: One way to fix the cross-contamination is to run straight water from the dispenser for a little while. But that brings you back to problem #1.