I was going to be a little quiet about this, but regarding the controversial topic on the "3ds limitations" I've gone ahead and done some research on the hardware specs of the wii u, wii, gamecube, and 3ds.
I honestly doubt that space is an issue-- but I did think that perhaps RAM or processing power would be a problem on the 3ds. If you examine the system specs of the Wii and 3DS, you can see that the 3DS is actually more powerful in quite a few areas. For one, the 3DS actually has more RAM than the Wii does and is more efficient at rendering graphics (shaders and textures) than the Wii is. However, when it comes to raw MHz, the Wii's processor clocks in at 729 MHz, while the 3DS trails behind at around 268MHz. The 8gb on a 3ds cart should be far more than enough space, and the 128mb of RAM that the 3DS has is a significant upgrade over the Wii's 88mb of RAM. The Wii U leaves both of these systems in the dust with it's 1.25GHz processor speed along with 2GB of RAM though.
So what does this all mean? It means that Sakurai is going to have some serious problems when it comes to loading times and having multiple things on the screen. I'm talking frame rate drops and unbearable transformation sequences when it comes to things like zelda and sheik. Sakurai is NOT saying that he's going to need to reduce the roster size because of the 3ds, and he's NOT saying that he's going to need to find ways to save space by removing cutscenes-- he's saying that the way some characters (or other aspects) innately work is going to need to change/ be lessened in some way in order to make the gameplay on the 3ds version as smooth and seamless as it is on the wii u version. This could mean things like Zelda and Sheik could very well perhaps only be switched on the character select screen instead of midway through a fight, or that Olimar would only be able to have 2-3 pikmin out at a time, or even no pikmin at all and have a completely revamped moveset. It could also mean that the Ice-Climbers may just have to be reduced to a single Ice-Climber, or that PT would only be able to choose one pokemon per fight, or even outright cut from the game. These are the kinds of "reductions" Sakurai is referring to. He is not talking about reducing the number of characters in the roster. If he plans on having both consoles have "identical" gameplay (ie: characters, movesets, etc), then some things are going to need to change to make sure the 3DS can keep up.