I can sort of see why people wouldn't like clones; if you want a character in you probably want them to have a unique moveset. In the case of someone like Ganondorf, I can totally get why you'd rather he be in with a distinct moveset rather than be Falcondorf. I used to be pretty anti-clone character myself and I still think the Falcondorf situation is pretty weird.
I also think it makes sense to have preferences when it comes to what clone characters get included. Dark Pit seems to be a controversial choice, at least partly because he comes from a game Sakurai developed. If I were in charge, would I have chosen him? Probably not, haha, since as a Pikmin fan I'd rather have Alph.
But honestly, the more I play Smash 4, the more I appreciate all of the characters in the roster, including DP. While I don't play as everybody regularly, I think every character/alt adds something to the game, whether it be offering a completely new or slightly tweaked moveset or giving more people a chance to play as their favorite character. For example, though the female alts for Villager and Robin play exactly the same as the male ones do, they let people who prefer that version of them (and/or identify with it) be able to use the characters they like the most in Smash. I think there's definitely some value to that, just like there's some value to letting Falco fans play as Falco and Lucina fans play as Lucina, regardless of how original or unoriginal their movesets may be.
As for clone characters, Sakurai's statements about how they're made, as translated by the people on SourceGaming, have convinced me that they're really just a nice bonus. Like alts, they give people more options and allow more people to play as their favorite characters without cutting into a ton of development time that could've gone to characters with unique movesets. In my mind, that's a good thing.