Stop that. There are no "slots." It's not "Well, we were going to put in Ghirahim, but we decided on Dr. Mario instead, and we can only have X amount of characters." It's "Is Ghirahim worth putting in the game?" Not to mention the fact that clones require considerably less effort and resources to implement compared to unique characters, meaning that even if there were "slots", a clone making it in doesn't necessarily mean a unique character could have made it in their place.
There's no finite number of slots to be "taken up" by characters. I mean, theoretically there are the limits of the system itself, but I think that number far extends any amount we'll see in the game.
Don't get me wrong, I like an aesthetically-pleasing character select screen, too, but making it look cluttered is really the only consequence of having clones take up an additional space.