Somehow I doubt that the game forcing them to be used without customs in one of the settings is how anyone decided they didn't want customs, but we'll have to agree to disagree. Honestly where the current state of things is that Miis are disallowed entirely, I find the idea of allowing their inclusion on the terms that they just follow the same rules as every other character a much more reasonable idea.
As a side note, I suppose I should explain a bit more on why I disagree on the "but it's allowed" argument. I mean, really think about it. Items are allowed by game defaults. Coin matches are allowed within the game. There are many more stages allowed than what tournaments use. As far as I can see, the community has always been fine with limiting what the game "allows" if they considered it to give an unfair advantage (or if it made victories less dependent on player skill, but that's less relevant in this circumstance).
Also, on the argument of the Miis having no default settings... eh, yes and no. When you create a Mii (In SSB4, not creating the Mii in general) you are taken to the character customization screen. While this screen does allow you to choose any of the customs immediately, you are not require to alter anything to complete the Mii. Should you choose not to go into these customization menus at all, they are all left on 1. So... eh, like I said, yes and no, I could see it arguing either way. After all, every character can get to a customization menu before you use them for the first time, doesn't mean that you can pick whichever ones you want to be their customs-off set.