I was expecting online lag in this thread, but I'll explain both terms.
One is frame rate drop. Only a few 3DS titles like Mario Kart 7 and A Link Between Worlds are able to maintain 60 FPS with 3D on. Considering how chaotic Smash can be, we can only hope it'll be 30 FPS with 3D on and 60 FPS with 3D off, which should be the ideal performance. The reason why the 3D effect causes drops is because it has to render twice the image, and so the 3DS has to do more work. Optimisation also comes to play here, so Sakurai will need more time in development in order for that to happen. Also, Pokémon X and Y is a different story because it was rushed and wasn't optimised well given the amount of bugs it had during its release. But yeah, the amount of polygon and animation effects contribute to slowdowns during battles.
The other is online lag. The 3DS, as well as Wii U, utilise the Nintendo Network. It's obviously better than Nintendo Wi-Fi Connection, so we should expect better performance on this as well.