While KI:U is very very good, it's still a tiny series. Two games isn't anything to boast about. A second rep isn't warranted in the same way is was for say, Mother, because Pit represents every aspect of the series by himself. I'm not making any predictions or calls here, but I would be very surprised for any series to effectively get the same number of playable characters as there are games of that series.
For the record I'm aware of Myths and Monsters, but for all intents and purposes Sakurai isn't. The game wasn't released in Japan and no reference was made when Uprising came about. I wouldn't be quick to count it as being of much significance.
When I talk about series size, I usually don't refer to amount of games, as they can vary wildly due to how game development works. I don't think Pikmin is a small series, but under the size argument it is because it's only had two games released so far. Some games tend to have one release per generation, so that would make any game from only one generation small, but that's clearly not true. The Wii Sports series has only had two games but sold over a hundred million.
I'm thinking KI is a bigger series in the game prominence sense. Kid Icarus is much more prominent in Nintendo's eyes than a great deal of other series. It was the only series included in Smash 4 that wasn't a newcomer or one of the original eight. They could have put Fire Emblem, Mother, F-Zero, etc, there, but they chose KI. It's a very deliberate decision that shows Nintendo believes in its risen profile. I don't know if that translates into another character (and your logic is pretty sound on why not), but Brawl showed that they are more willing to expand the amount of character in franchises than add new franchises. As one of the series with only rep, its natural to think it might be one of those series. But it's definitely not a small series.