With the quality of the average game, it'd seem the 3DS is weaker. The only game that's been released that's comparable to what's been on the Gamecube is Revelations and I think Resident Evil 4 looks better in aspects, including character models.
Not only does RE4 on the Gamecube look better, but the 3DS version of Revelations has very noticeable frame drops whenever loading new areas and even runs sub 30fps a lot of the time throughout the rest of the game.
*edit*
Another thing worth mentioning is that with Pokemon X and Y, in combat, the game will often run at around half the framerate. If you pay close attention you can also notice framedrops on the world map.
If you're interested in checking out a location where there's a drop in frames on the world map, fly to the town next to the daycare center and then walk across the bridge and keep walking after the daycare center comes into view. You don't need to be up at the top portion where the screen will look into the background, but pay attention, you'll notice a quick framedrop and then it'll pick back up. Walk back right you'll notice it again. It's specific spots in the game you'll notice frame drops which makes me think it's allocating new textures into the games ram.