You know, I've been thinking about these new ones, and I would not be surprised if a number of the "bad" ones actually increase in popularity when they make their Anime debut. The reason I say this is because it has happened before. The Anime tends to have a completely different art style than that of the games.
One such incident was with the pokemon Mawile.
When this pokemon first appeared in the games, it just looked hideous. You seriously could not love it. Basically, it all had to do with a bad angle that did not show off the beauty of the pokemon. The popularity for this pokemon did not look good. That is, until it's big debut in the Anime.
If you ask me, they did an excellent job bringing out Mawile's true beauty. From there, the popularity of Mawile just skyrocketed. There seems to be an endless number of fanarts of Mawile out there today. (Turn Safe Search On if you're going to look. This pokemon has a good amount of porn.) You can even find well crafted flash video of it. There's even a good amount of webcomics with it now.
Oh, and one last thing, Mawile is often portrayed as a "she" by fans. Considering the look, not surprising.
There are indeed other pokemon that owe their popularity to the Anime, where the games nearly killed them. I wouldn't be surprised if the Anime can do the same for some of the newer pokmeon.
