To me especially, Smash Bros. makes a big representation of all of Nintendo's great series, and I feel some of them are a little bit under-recognized - as in, they don't contribute enough characters made playable in Brawl. (Assist Trophies and Boss Battles are good ways to shove a few more in.)
Metroid is a great example here, as it is one of Nintendo's best and most popular series, yet the only character from it who's playable in Brawl is Samus. I understand she is usually the only character in most Metroid games (aside from bosses that really CAN'T be made playable), but some of the newer games like Metroid Prime Hunters and Metroid Prime 3 introduce other bounty hunters - and we already know Metroid: Other M will have a few more characters. Metroid Prime 3 was released a bit too late during Brawl's development, so it contributes nothing, and Hunters isn't distinguished enough, so that's a good excuse to include no other Metroid characters. It does emphasize the "loneliness" well. I expect to see more of them (likely other hunters) in the next Smash Bros. game, though.
F-Zero is another series that's a bit under-represented character-wise. Captain Falcon is the only one. It's not their most popular series and does seem to be fading, but it's heavily centered around its characters and has many to contribute. It's at least fair to see some of the original four from the SNES F-Zero. (The other three being Dr. Stewart, Pico, and Samurai Goroh.)
The EarthBound/MOTHER series isn't terribly underrepresented (at least, as far as this game goes - it even has a boss), but there's ONE more character that I feel must bee here if Ness and Lucas are: Ninten. If they have the main heroes of MOTHER 2 (EarthBound) and MOTHER 3, then it's only logical that the main hero of MOTHER 1 should play a part, even if he does happen to be Ness's paralell. (As a side note, I don't know why they had Jeff as the assist trophy.)
Pikmin could maybe use more characters. I know there's some other little buddy with Olimar in Pikmin 2 who could also be here, though I forget his name (Louie or something like that?). I haven't played any Pikmin games, so I don't really know the emphasis on other characters or how well they would fit in Brawl. It very well could be that having just Olimar works perfectly. Maybe it also has that theme of being "alone" like Metroid does, but a little different seeing as you have the Pikmin (in both Pikmin and Brawl.) It might be emphasized more, too.
Animal Crossing has no playble characters in Brawl, but they do have their own stage. This is a different story, however. This is one case where it's appropriate to have so few (zero) characters, as it helps reflect the nature of Animal Crossing, as it doesn't involve any sort of fighting or even characters being enemies.
A few of the series with only one character still find it appropriate because of how old they are. Ice Climber and Kid Icarus were made back when games had few characters. The hero and the main villain were usually the only characters who fought at all, and the main villain was usually some huge beast that wouldn't fit comfortably as playable in Super Smash Bros.
R.O.B. and Mr. Game & Watch are both from their own thing, but neither is really a series or a single game as much as it is hardware - so, naturally, neither of them came with a whole host of characters. Their roles in Brawl would be ruined, or at least damaged, if other characters from the same "series" were included. Likewise, other Metal Gear or Sonic the Hedgehog characters would ruin Snake's or Sonic's role (respectively) as cameos in Brawl.
So, some more characters would be nice for many of the series, while some that are low in numbers don't really need any because the character is meant to be distinguished, or was simply the only character from that series.
