Invent a mechanic for Baby Pokémon which would make them competitively viable. Could be an automatic thing, or an item, or an NPC who powers them up when you talk to them.
Hard mode: it's available for the entire game but isn't that useful against NPCs, only against actual humans.

Suggestions
>Fifth move slot
>Half damage from all sources
>Immune to status conditions
>Babies always move before non-Babies
>Increased accuracy, letting them make use of attacks their evolved forms couldn't
>Customize their typing
>Support abilities that only function in Double Battles. E.g. Friend Guard + Propeller Tail + Telepathy all at the same time.
>Babies' moves bypass screens and/or substitutes