The 3DS and Wii U specific controllers all have true 360 degree movement, but Smash 4 specifically reads only 8 directions (though analogue for those directions). What ends up happening is the software is doing some math to figure out where the threshold is for one direction, and your hand movements cross that threshold. It's something I notice back when the N64 first came out and many gamers were getting used to it. In this particular case, the way you hold your 3DS for movement is making it so certain actions are harder to move accurately. Think on how your thumb moves from left to right on the Circle pad, and notice how it is an arc and not a direct left - right. This is actually what is getting in the way.
You'll want to train your hand to move the circle pad more like a D-pad for it's directions instead of an analogue stick, which will help. (The circle pad is closer to the unit, so it has no circumference to need to be applying pressure against to work.) That helped me when I was first getting used to the Circle pad when I got my 3DS.