Rancid suggested that all pets should be able to fly or swim. I disagree with that all pets should be able to fly or swim flawlessly.
As a solution, I think they should all have the crosswater option. Their swimming skill should be based on their level. Let's say a level 15 pet would have 100% swimming skill.
Separately, I think certain pets should retain the aspects of their origins. All dragons should fly (that's a given). All air and wind elementals should be able to fly as well. Water elementals should have 200% swimming skill. Fire and Plasma pets should never swim in water.
Let me know what your thoughts are on this.