This seemingly innocuous effect is introduced when a game confronts players with a roster of monsters to collect - normally numbering in the upper hundreds - with having no clear bearing on the game's plot other than padding out the overall run time. While a fully stocked compendium is - strictly speaking - optional in all of these games, it's a fresh hell for someone obsessed with scoring a perfect game.
Pokemon isn't the only sort of game to inflict this torment on players. The Shin Megami Tensei (and by extension, Persona) series of games always has a vast amount of demons for players to collect, fuse, and otherwise evolve - although it usually hides it under a dark and mature storyline.
Still, the collect 'em all mechanic works seamlessly into the games, and it's a lot of fun for the challenge, but I'm always surprised at how quickly it wrests the focus from the story and places it directly on the collecting aspect.
I don't even know what she does, and I'll probably never use her, but I *need* her in my compendium
I've confessed to being a completionist before, and I'm clearly not alone when I fall for these types of games - but I always find that I'm disappointed with myself when I completely abandon the story of these games to focus instead on collecting as many demons as possible.
Yet the developers shouldn't be chastised for this game mechanic, since it still provides plenty of fun for players who don't mind spending hours crawling through dungeons in search of a missing demons or Pokemon. But these developers should take a step back and realize what ramifications The Pokemon Effect has on the overall narrative of the game itself.
Much like how Final Fantasy VII presents players with sprawling, optional sidequests to complete as the meteor hurtles toward the planet's surface, Shin Megami Tensei and Pokemon games lose their sense of urgency when they give players limitless hours to spend collecting missing entries in their Pokedexes/Compendiums just before the final battle.
Still, there will always be completionists who view the final battle as an anticlimactic affair (I think I steamrolled Sephiroth at level 60 in under 2 minutes last time through FFVII), and for these players The Pokemon Effect presents an additional layer of depth and challenge to the games.
...even if you know - deep down inside - that you're just racing chocobos around the Golden Saucer when you really should be saving the world.