Honestly, I think custom colors would be great for Smash 4, if executed correctly. It will give us a more personalized character, and try to differentiate our mains with the mains of others. Plus, how often have people fought over which character color they want to go with in a Smash Bros. game? I'm sure the arguments over color choices weren't anything major, but a character's color scheme that fits the liking of the user can be quite significant, even in the way the player performs in the more extreme cases.
Also, Sakurai did mention wanting the 3DS to be more personalized and also threw in the word "customization" as the main point of it, so it can stand to reason that colors could very well be something that can be customized in Smash 4.