Adding on and slightly changing Mr creeper and co 's Legendary Idea I have come up with a better idea. When a player does /claim he/she has a 0.1% chance of getting a shard from their respective team like valor for example. After getting 5 shards they could go to a NPC to exchange them for a legendary. The legendaries for claiming would be team related so eg. Valor moltres. The NPC in Kyoto would give a legendary bird if you exchanged in gen 1 and In jatoro the NPC would give one of the legendary dogs. However being obtained by NPC the Pokemon would be un-trade-able. Just a thought.
I was think more of doing quests over chance to obtain legendaries pokemons. But only receiving the legendary bird depending on your team is a pretty interesting idea