I don't like them because they're completely unnecesary at this point (due to the humongous amount of characters already in the game), and because they sometimes kinda cheapen the character that was made a clone in some ways.
For one, Ganondorf got into Melee as a clone. If he wasn't a clone, he wouldn't have gotten in at all.
But now that he is in multiple games and half of his moveset is still taken from Captain Falcon, while having none of his iconic moves from his own games... Was that really a good thing to happen? Wouldn't it have been better to leave him out of Melee, and add him on Brawl where there would likely have been more time to properly develop his moveset? It's already too late to change him, his moveset is an established part of Smash. Did it really have to be like this, though? If they actually had been time to make Ganondorf a full character from scratch, would he have been anything even remotely close to what he's like today? Most likely not, so I question the decision to make him a clone in the first place.
There's a similar situation with this game's clones. Most notably with Lucina. Lucina may have posed as Marth for a while in her own game, but she's her own character. She has her own fighting style. She has her own moves. She doesn't even use her own fighting stance in this game! But now that she got added in as a Marth clone, she'll probably stay as one even if she returns for the next game. Even if she gets different animations and stats to make for a different kind of playstyle, that Marth base will always be there. It's a far less extreme case as with Ganondorf, as at least she's from the same Franchise as Marth, and they both belong to the Lord class. But it's still going to hold back the full potential of Lucina as a unique fighter if they choose to bring her back in the future.
Dr. Mario I just find a lame clone because he's literally Mario with a different costume. I find clones fun when they add a new character into the game. Otherwise, why bother?
Dark Pit on the other hand? I think he's a good clone. Kind of a weird choice considering that Kid Icarus also got a newcomer in this game, but he's a good clone anyway. I mean, he's a different character from Pit, but personality aside he's basically exactly the same as him in their own game, having the same moves and playstyle makes perfect sense to the point it would be weird if Dark Pit got into the game and he wasn't a clone. Or a semi-clone at the very least.
At the same time, Dark Pit is a huge waste of a potentially great clone because of how much they held back on the changes. Other than just a few moves with slightly different properties, he plays exactly the same as Pit. But judging only by the clone choice, I think he's by far the best clone in this game, and I actually hope he returns in the next Smash game with his own twist to Pit's playstyle, or even some Luigification.
If you ask me, the best example of a good clone in the Smash series both in choice and execution, is Falco. Falco is not only from the same franchise as Fox, but he's a part of the same team. It's only logical that he uses the same equipment and even fighting style as Fox. But of course, he also has a different personality, and that's reflected in his moveset too. As a member of the Star Fox team, he fights a lot like Fox, but brings his own personal twist into the fighting style, and also has different movement speed and jumping height to further reflect that. It just makes sense.