Hack name: Pokemon: Rocket's Revenge (by EarthsVisitor) (Part of the staff, though it looks great still)
I would vote for Pokemon: Battle Fire by Concord, but since it just got posted onto PokeCommunity, I wouldn't find it fair.
Reason for nomination: It has a very good storyline. Where you get to start as a Team Rocket Grunt, and climb the 8 Missions and gain Ranks (Missions and Ranks instead of Gym Badges). And as you gain the Ranks, you get different clothes, and start out as a Grunt, and end up as a really big part of the team.