There's good clones and bad clones in my opinion.
Dr. Mario is someone I see as a bad clone. Why? It's just not adding any new character into the game, that's still Mario, moveset differences or not.
Dark Pit is kinda sorta okay? He's a different entity than Pit at the very least, but considering they're canonically nearly literal clones of eachother, I don't think there's much reason to add him in. His existence doesn't bother me, though, and I even think he would have been a great choice if it wasn't for Palutena already giving us extra Kid Icarus representation. I don't hate this guy like I do Dr. Mario, but I feel like he's completely unnecesary.
Lucina is good clone. We get a completely separate identity, and a slightly different playstyle for better variety. I doubt I'll use her too often, as I think of Marth's tip-sweetspot thingy as his most fun feature, but she's cool.
Toon Link, also a good clone. There's a lot of different incarnations of Link, and this is the best way to represent that. Just like in Zelda, you have similar gameplay and a few shared iconic weapons, but there's a general feel on each game that gets translated pretty well in here. If we had three Links, or an extra alternate version of a character (like a Toon Ganondorf/Zelda) that'd be another story.
Ganondorf? Worst clone in the history of crossovers, for real. At this point, he has very different style to Falcon, but the fact that he's similar at all makes absolutely no sense because of who he is as a character. It was fine back in Melee, as that was the only way we would have gotten him, but now it's just weird. At this point, it would have been better for him to just sit out of Melee and join in as a unique fighter in Brawl. No Ganon once is better than clone Ganon forever.
So yah, that's my take on things.