The problem with wild empathy is that sigificant encounters with animals generally last a much shorter time than 1 minutes (the time it takes to calm the animal down).
Usually if party sees a hostile animal, they just kill it, or its already attacking.
If it isn't hostile, you don't need wild empathy (much).
It would work in the following situations:
1. stalked by a predator
2. a 'roleplay encounter' with an animal where it isn't hostile initially, but you need something from it, near it and it will become hostile if you go for it.
3. when the animal is WAY above the party's EL and the best course is to avoid attacking
The GM has to prepare specific animal encounters than make wild empathy 'work'.
Along with animals in the MM, we need a Disposition Chart and an animal goal chart. Roll some more dice and the DM can improvise