But will it make the pokemon appear in 3D?
The 3D feature adds a lot to some games. The new Zelda makes heavy use of the 3D and a lot of the puzzles would be harder without it. Games like Pushmo are basically mandatory to have 3D in order to play it.
Here's a list of top of the line games on the system off the top of my head, yes there are more than this... and the system has only been out 2.5 years, it has many years to produce more games. The games in bold are essential 3DS games in my opinion (Fire Emblem: Awakening being one of the best games I've ever played):
Super Mario 3D Land
, Mario Kart 7
, Resident Evil Revelations, Kid Icarus Uprising, New Super Mario Bros. 2, Professor Layton and the Miricle Mask, Fire Emblem Awakening
, Etrian Odyssey IV, Monster Hunter 3
, Luigi's Mansion Dark Moon
, Animal Crossing New Leaf, Mario and Luigi Dream Team, Pokemon X/Y, Pushmo, Bravely Default, Phoenix Wright: Ace Attorney: Dual Destinies, Theatrhythm Final Fantasy, Zero Escape
, Mario: Sticker Star, Donkey Kong Country Returns
, Kingdom Hearts 3D, Shin Megami Tensei IV, Tales of the Abyss, Harvest Moon: A New Beginning, Project X Zone, Castlevania: Lords of Shadow - Mirror of Fate, The Legend of Zelda: A Link Between Worlds