Buneary likely has lower than normal base friendship because it is a Friendship evolution. According to the Pokedex, both Buneary and Lopunny are cautious creatures.
Buneary:
When it senses danger, it perks up its ears. On cold nights, it sleeps with its head tucked into its fur.
Lopunny:
An extremely cautious Pokémon. It cloaks its body with its fluffy ear fur when it senses danger.
If you were already a high-strung Pokemon and some trainer came and stuffed you in a Pokeball, you probably wouldn't trust or like them very much, so Buneary has lower than normal friendship.
