Well, to be fair, the huge amount of KI enemies is because they were easily ported from KIU, which is also on the 3DS and likely running on a similar engine. Seriously, as someone's played KIU, the game feels a lot like Smash in many aspects.
While several other enemies are also ported from 3DS games, such as most Ocarina of Time enemies from the remake, they still were given new animations and were worked from scratch in regards to AI programming.
That isn't the case with the KIU enemies that have their models, animations and even some AI ported directly from KIU. They provided variety to the mode and was a time and cost efficient way to add more enemies to the game.
Sure, it skews on the balance between series, having more enemies than even the Mario series, but it adds to the gameplay,
the most important thing above everything else. The development team had a huge amount of easily usable resources from a previous project at their disposal that also could serve a purpose on a new project. They didn't just let those assets go to waste, they put them to use in a way that benefited the game.
Likewise, a bunch of SSE enemies were also ported from Brawl (including some Mario enemies like Goombas), but those had to be downgraded to work better on the 3DS hardware.
Of course, the ideal would be if every series had the same amount of enemies as Kid Icarus does, but I don't think there's much room to complaints considering the above circumstances.
After all, this is the most varied and most crossover-like enemy roster we've ever had in Smash and a huge step above the enemy rosters from Melee (which only had a few enemies from Mario, Zelda and Ice Climber) and Brawl (which was entirely original stuff aside from a few Mario enemies).
We have enemies from Brawl's SSE, Mario, DK, Zelda, Metroid, Kirby, Pokémon, EarthBound, Ice Climber, Rhythm Heaven, Kid Icarus, Pikmin, Mii series and even third-party franchises Sonic, Mega Man and Namco arcade classics.
From a Q&A article with Sakurai himself:
Source:
http://www.sourcegaming.info/2015/07/09/i-answer-some-questions-sakurai-famitsu-column-vol-461-464/