My biggest picks would be:
#1) Pikmin - The latest brainchild of the man that made Nintendo what it is today. Olimar being playable and an AT or two are a must, no doubts there.
#2) Fire Emblem - The series that started the entire tactical RPG genre, one of Nintendo's longest-running franchises, with a size rivaling Zelda and Pokèmon discounting remakes, popularity in Japan that rivals Zelda's, and now since its international release moderate popularity elsewhere. Marth's return and Roy getting an AT slot is the bare-bones minimum of what the series deserves beyond what we presently know, and a third character ought to be in if the roster is at or above 40 characters.
#3) Metroid - If the only new character this series gets is a Samus transformation, it'll be as big of a travesty as Diddy's absence from Melee. Another character is a must, and a couple of ATs sure wouldn't hurt either.
#4) Donkey Kong - Diddy is a huge step in the right direction, but this is Nintendo's #4 best selling saga ever, only recently usurped from its former #3 spot by Pokèmon. K Rool ought to be at least an AT, preferably playable, and Dixie or one of the other Kongs would be a good choice for an AT.
#5) Star Fox - Obviously its guaranteed at least one more PC from among its three remaining candidates, but with how popular it is it deserves two, and the third ought to be an AT if he/she can't be playable. Either Corneria or Sector Z should return as a stage, too, since many fans prefer them to the new one from what I've seen.
#6) Golden Sun - A newer series, but one with plenty of loyal fans still hoping for it to continue, and one which Nintendo and Camelot have said they're interested in continuing. What better way to honor it and get the ball rolling on its continuation than with Isaac as a PC and one or two others as ATs?
Note: I also believe that all series with even one playable character should get at least two stages, which was the count in Melee for everything but Fire Emblem, which only missed out due to the rushed nature of the game.
Zevox