I think from a technical position, all the mounts are programmed to run at the same speed. However, due to individual aspects of certain mounts, some seem to run slightly slower or faster than others (this is most noticible with mounts that are low to the ground, like the cavalry drake and coruel - because they're closer to the ground it seems they're faster. However, the taller ones like the goobbue and magitek armour seem to be much slower due to their size.

And for reasons I haven't yet deduced, my Legacy Chocobo seems to run slightly faster than the default Grand Company chocobo, but that just might be me looking for things that aren't there.