Idea for a Pokemon Status Condition: Infection
Think of it like a non-lethal form of rabies.
So you know how in some games, Pokemon above a certain level will ignore you as a Trainer until you reach a certain point in the game? Infection plays with that a bit. An infected pokemon doesn't just ignore the Trainer. It turns on the Trainer! As the player, you either have the option to send another Pokemon out to defend yourself, or to run away. This determines what happens next.
1) Send another Pokemon in: if the defending Pokemon causes the infected Pokemon to faint, the infected Pokemon can go back into its PokeBall and be taken to a Pokemon Center for healing. This cures the infection. BUT: there is a small chance that landing a direct hit on the infected Pokemon will cause the infection to spread. Think of it like Static or Poison Point.
2) Run Away (or lose the battle against the infected Pokemon): the infected Pokemon roams. It travels back to the nearest wild area where you caught/obtained it (so a Kanto Starter would go to the grasslands outside Pallet Town). This is where you have to go to get your Pokemon back. You don't have to catch it again, but making it faint will return it to the PokeBall you had been using to store your once loyal teammate. Once in the ball, it can be healed at a Pokemon Center. Do this if you don't have a team with super effective moves against the infected Pokemon, perhaps.
Either infection is part of an evil team's plan to ruin other Trainers' days, or it's an naturally occuring disease that the region hasn't figured out how to cure yet. The only other thing I have to add is that Pokemon with high Friendship resist infection while Pokemon with low Friendship (who hate their Trainer) are more likely to suffer the infection. You can also attempt to help other trainers faint their infected Pokemon so they can be healed (with the obvious risk the infection spreads to your Pokemon).
What do you think? Can you imagine a Pokemon ROMhack with this mechanic?