For me, for some reason, i kept accidently jumping when i was trying to do a forward smash, really threw me off all the time
*grabs classic controller*
That's just the round shape of the controller affecting your grip, and the position at which you hold the control stick. Like I said, the GC controller has an easier-to-reach stick, which makes movement and attacks feel more natural. The Classic controller has your thumb at an odd angle, and may take some getting used to before you stop accidentally hitting the stick at a diagonal whenever you move it to the right.
From an outside point of view, I can see most Melee owners using the GC controller because they're already used to it. (I'm actually just using it for the rumble, like Sakurai) Newbies to the series will likely gravitate to the Classic controller or the Wiimote/Nunchuk because they already own one, and it means they don't have to deal with the wires. It's an even trade-off. Nobody will play with just the remote. That would be stupid.