I think I just had a cool idea for a pokemon game plot. The main premise involves finding and catching rare pokemon, think nosepass, chimecho and feebas in hoenn, not necessarily legendaries.

It could start out with the professor calling you to his lab and telling you and the two rivals that three rare pokemon have shown up in a neighboring forest, the starters. He will show you pictures and ask which one you wanted to go after and give you a pokeball. The meek rival will go after the one strong and the hotblooded rival will go after the weak one (and always get upset when he loses to you). You will then go to the forest, which is just one room and catch the starter with a scripted auto catch. Then you will battle the rivals ect.
Progression blocks will involve catching rare pokemon for the professor, I.E. after you catch a rare nessie based pokemon or something he will give you surf to get to the next town.

The evil team could maybe be led by a rich eccentric who hires "poachers" to catch pokemon for his personal zoo, which has the pokemon living in poor conditions in the basement of his mansion. The climax could involve liberating them with your rivals.

I think the early villainous encounter could involve the team trying to steal a rare pokemon that the professor asked you to bring him.

I think this would be a neat idea since catching em' all has not really been the focus of the games lately.

So ITT: post your pokeplot ideas and help others expand theirs!