I think a tier system that could include EVERY SINGLE POKEMON in the game would be cool; it would provide lots of opportunity for fun and versatility. How's this:
1) Uber
2) OU
3) BL
4) UU
5) NU
6) Rookie Uber (e.g. Meditite, Murkrow, etc)
7) Rookie OU
8) Rookie BL
9) Rookie UU
10) Rookie NU (e.g. Caterpie, Weedle, Magikarp, Sunkern and other poor Pokémon)
I'm calling it "Rookie" instead of little cup, because it'll be more flexible in adding evolved Pokémon to shine as well.
What do you think? Please be positive!