I would say that Protect is a very good option as it allows you to burn your foe and alternate between Wish, Protect and Acid Armor for healing and set-up. On the other hand Baton Pass is good for passing Wish and Acid Armor to a team mate.
If you want you Vaporeon to be a Team Support Pokemon, go for Baton Pass.
If you want your Vaporeon to be a Stall Pokemon, go for Protect.