Entei is incredibly Badass and intimidating....and also the biggest teddy bear in the whole Pokemon world. He's got a bigger heart than almost every "real" Pokemon seen so far.
Entei: If that is what you wish.
Entei: I am happy that you are happy.
Sure, Entei might not actually be her dad, but they certainly treat each other with all the love of father and daughter. Even when the rest was forgotten, this Troper still remembered the scene where Entei turns Molly into a teenager so she'll be stronger.
When they first met, Molly confused him with Spencer and called him Papa for the first time. After a moment's confusion Entei is perfectly happy to play the part.
Entei: Papa? (smiles gently) If that is what you wish.
This troper always chokes up a little near the end of the movie, when Entei is trying to help them escape the Unown.
Entei: The last thing I can do for you is to take you out of this place.
In the beginning scene of the movie, Spencer and Molly playing together is quite possibly the sweetest thing in the history of ever.
Molly reuniting with her father during the ending credits…then with her mother as well, as Molly runs into her arms. It was all the poor girl ever wanted.
In that same moment, Molly is playing with a Teddiursa. It looks like she was given a real one as a present.
Charizard hears about the battle with Entei and leaves Charicific Valley to join the fight and save Ash and Pikachu.