Every single one of those things would take at least 10 times as much time as copy/paste, change a few values, add a couple new animations.
If these characters weren't added we would have likely gotten absolutely nothing in their place.
Which was the majority of the list. Copy/Pasting, changing some values, and adding some new animations to existing characters.
"Or balancing the game even more
Or changing Ganondorf so he would be less of a clone
Or giving Falco an arwing for his FS
Or giving everyone alternate costumes
Or more palette swaps
Or giving Sheik a new FS
Or giving Toon Link a new FS
Or giving (insert name) a good FS
Or adding more alternate costumes
Or having one unique semi-clone instead of three clones
Or more customization options
Or perfect the current roster then add even more clones as Free DLC
Or overall improving many aspects of the game as possible before having fan-service/roster padding."
Why would any of these things take longer development time than three clones when they both have the same process?
In most game development projects, character design is a separate team than stage, item, gamemode, etc design. Then characters development is broken into separate groups for concept, modeling, texturing, animation, and stats/implementation.
Creating clone characters would not have taken anything way from non-character aspects of the game, nor would it have taken much away from the concept stage (particularly because everything was built from the ground up anyway).
Your right about the non-character aspect, but what about the character aspect? With the time to make clones, they could have done more with that section of development
People who complain about clones wrongly assume that one day Sakurai sat down and said "hmmm what would be better... Ridley or Dark Pit? Dark Pit of course!". What ACTUALLY happened was Sakurai had a bit of extra time to add a bit of bonus content into the game and thought that fans would be happy with a little more. so stfu about the clones because you lost absolutely nothing from their inclusion
Again, that's a false generalization.