I'd say Metroid and DK are severely underrepresented. We've not gotten much in the way of either series since SSB64, always a jungle level/lava level, always the same sounding remixes, no new characters until Brawl, and none since, and the conspicuous absence of a major villain.
Star Fox also could use a bit more creativity, particularly in the Final Smash department.
I'd also argue that Zelda is slightly underrepresented. In terms of characters, they're perfect (but I'd love to have Ghirahim and Midna to round out the 'Minor villain' and 'Exposition fairy' types). However, they're still hopelessly cloned from each other. This is the first game where Toon Link doesn't even get a unique crowd cheer! I think they need some love in decloning, particularly after Hyrule Warriors showed us what we should have by now.
Overrepped: Fire Emblem a bit, but I have no problem with overuse of swordsmen. I don't like overuse of the same swordsman.
Also, Kid Icarus, but that's obvious. All the KI content is from the same game, which was the series' first in over 20 years. They make up most of the enemies in Smash run, have multiple Assist characters (DK is still waiting for its first), the Classic Mode was thrown out to make way for the new "Classic mode: Uprising, " and of course, that's the major stage with the codec. KI is a tiny 3-game series, but makes up the majority of content rivaling Pokémon and Mario.
I think Mario and Pokémon are repped fine. They are both Nintendo's massive flagships, and should be repped accordingly. Also, it's ok to have Gen 1 repped more than the others, since that's the first one, and most Smashers who are 25+ know the older ones better than the newer ones.
Just because the clone took less dev time doesn't mean it took none. It still had to be made, and people who are not good with the parent now have to play the same character essentially twice for certain challenges. Let's also point out that BOTH of the Marth challenges are on the top row, and one can't be hammered. Good luck to people who are not good with Marth but want to collect everything.
And I'd wonder what would happen if instead of DP and Lucina, we'd gotten K.Rool (Bowser) and Ridley (Charizard) clones...those series would get the representation they need, the KI/FE series woudn't get the overrepresentation that's killing support for further KI/FE characters, and then the people who like large reptilian bosses would finally get something... I don't think we'd be having these arguments.
Of course then in SSB5, we'd be arguing the same as we are with Ganondorf now, that he needs to be decloned...
). Aside for that joke, I would like to see at least Goroh, or one of the ideas exposed by 
