Maybe you should have placed specific categories on what pokemon gets beaten brownie,Because you are only asking what beats pokemon in GENERAL, lease add categories to diversify the conversation:
For the musicals (BGMs): ties with The Legend of Zelda, Kingdom Hearts, Madworld (only on Wii) and the Ar Tonelico Series
(Compares to Pokemon Mystery Dungeon Series, Pokemon Conquest, and Pokemon Main Series [especially the unova saga])
For the Story Plot: Ties with Final Fantasy Series, Kingdom Hearts Series, Legend of Zelda Series, Fire Emblem Series, The Legend of Legaia (PS1), Fire Emblem series, Ar Tonelico Series, Assassis Creed series, and the Mario RPG series like Partners in Time and Bowser's inside story.
(Compares to Pokemon Main Series, Pokemon Coliseum and XD Gale of Darkness, and Pokemon Mystery Dungeon Series)
For the Gameplay Mechanics: Cave Story [in Japanese, it is said as Doukatsu Monogatari. try it. its great], Madworld (only on Wii), and Fire Emblem Series surpasses Pokemon. It ties with The Legend of Zelda Series, Harvest Moon Series, New Super Mario Bros Series, Minecraft, Mario and Luigi RPG series, Metroid Series, Assassins Creed Series, and Disaster: day of Crisis (a Wii game never going to America)
(Compares to Pokemon Main Series, Pokemon Snap, Pokemon Coliseum and XD Gale of Darkness, Pokemon Rumble Series, Pokemon Mystery Dungeon Series, Pokepark Series, and the Pokemon Trading Card Game)