Because none of the "clones" are actual clones. Functionally they are completely different characters with the added advantage of requiring significantly fewer development resources than a completely original character would. Even if you got rid of all of them, there's no guarantee you'd free up enough dev time to properly implement a single all-new character.
I mean, no, they are clones. I don't know what you think "clones" mean, but from a fighting game perspective they are 100% pure clones. Lucina is especially literally a re-skin, except her sword has flat damage instead of Marth's tipper. They share identical moves for most of their specials, they have the same standard attacks, air attacks and fighting/moving animations. Dr. Mario and Dark Pit have one unique move each - Dr. Mario clones Luigi's down-b and Dark Pit clones Zelda and Shiek's final smash.
That's not a bad thing though. Sakurai has recently used the metaphor that creating a character is the equivalent of creating a large meat dish for a meal, while creating a clone is the equivalent of creating a small dessert. They require significantly less work to make. Only Lucina was ever planned as a clone too - Dr. Mario and Dark Pit were last minute additions to the roster.
Basically, the people in this thread complaining that they took the slot of another character don't understand how game development works.
It was really hard for the first few hours, but after that, it just became easy. I could kill anything by the time I reached the second region, so the nemesis system really did nothing for me from then on. If by chance a captain would kill me, I would just go find them and kill them straight away to get revenge.
It's a shame, I was forced to finish the game because I had no reason to play around with the nemesis system. The upgrades I picked were apparently too powerful and the runes I got were also apparently too powerful? for instance, I got a rune early on that gave me health for killing an enemy.
I know people will say to not use that rune or don't unlock the double finisher skill, but that's a fault of the game if me playing the way I wanted to ruined any sense of the difficulty. At that point I'm deliberating handicapping myself and if I'm having to come up with ways to make the game interesting myself, then something has gone wrong there. I want to play the game again so that I can go back to before I upgraded myself but the tedious and terrible campaign missions (aka 19 tutorial missions and then the final boss mission) just remove any desire for me to play.