To keep them safe from the weather and rogue Pokémon! I have to bundle up Sprouty during the colder seasons since he's become so use to the outdoors, and even though he doesn't mind the rain a lot of other Pokémon wouldn't like it... Rogue Pokémon can be scary too, if they're looking for a meal and yours is an easy target.

[Sprouty shudders slightly - he remembers all too well the trials of a Chikorita, with birds of prey swooping in. Brr.]

Plus it's easy to carry them around.