The "extra" characters are sporadic. There is no real precedence for who and why they got in.
We have 8 characters with unique models (and voices?) out of Bowser Jr., a former simple color swap got his own slot in Dark Pit, removed unique clones like Wolf. Removed PKMN Trainer for just one of the PKMN from that group.
Lucina, Doc Mario... Falco, dorf. Alph... I have no idea what the thought process was for the character selection.
Development and time restrictions are quite the cruel mistresses, I'm told.
No, really, development and how things progress can
greatly impact how the roster is formed. What they plan at the beginning isn't likely to be the end result unless they had another year of development. Certain things change in priority, members get shifted around, things are chopped completely in favor of getting the more complete stuff done, etc. etc.
I'm sure that's why we didn't get more alts. I'm sure that's why alts turned into full characters. I'm sure that's why certain characters didn't change at all from Brawl. At some point, you have to straighten your priorities out and it seems things like Bowser Jr's Koopaling alts took priority, likely because some of the work could have already been done and they were running out of time to get other things done.
There is no rhyme or reason for these things other than how things from the conceptualization/pre-planning phase can be completely altered and changed mid-development because of the shifting tides in how things get done relative to progress, time, manhours, the amount of people working on such and such content, etc etc.
Who knows how much time was spent on characters that didn't make it. For all we know, Ice Climbers could have had a whole month of work done on them only to find that they made the game nigh unplayable if there was more than one pair of them in a match only to scrap them completely and move on to someone else. For all we know, their number 1 priority was Smash Run for most of last year and characters were worked on on the side or stages were worked on much later in development.
That's why some of these things happen and why it appears "illogical". We only have to look back at Melee to see roughly the exact same thing. Smash 4 is essentially a repeat of Melee, except it's probably for different reasons or logistics behind the scenes we'll never know or have the privy of finding out (unless someone datamines the 3DS version lol). I mean, Brawl tells an interesting story with what was found on its disc with its leftover data.