While working on the vlan vtp training i noticed that the encapsulation kept switching around from isl to dot1q to the others, how do you know which one to choose and in an all cisco enviorment wouldnt you just want to stick with the same one and not having multiple protocols to try and keep track of?
I believe that in general it is better to use dot1q encapsulation. Some old implementations may have been done using isl and for compatibility you may maintain them using that encapsulation. And some models of switches support only one or the other. So in using these switches you must use the encapsulation that they support. If you really have a choice then choose dot1q. But sometimes you must work with what was there when you got to the project.