Smaller caliber paintballs also have a problem with range. Since they are lighter, generally, they have less kinetic energy, unless you increase velocity to make up for it. You could also make the fill more dense. So unless it is compensated for, .50 cal paintballs lob too much.
I believe that there was also a problem (as someone else alluded to) with the shell not breaking as easily as the ratio of shell thickness to caliber increases. The ultimate example is the airsoft paint pellets, which just don't break.
Once upon a time, there were enough .62 cal paintballs for there to be seperate velocity rules for them. I think it was either 320 or 350, but I am not sure. This may have helped with the range somewhat.
I also heard a rumor that the reason that the original paintballs were around .68 was that there were already bath oil pellets encapsulated in that size, so there wasn't a need to make a special encapsulation spindle for paintballs, which were not as in demand at the time anyway.