5/6 the Donkey Kong stages are jungles. Please understand.
We need a Metroid version of this where everything is lava.
There are definitely some issues with over/under representation. Let me just preface this nitpicking by saying that Sakurai and crew were probably under immense pressure and time constraint when developing fucking TWO of these games at the same time. One on a handheld that nearly explodes when you start it up. I don't blame Sakurai's team and Namco for pulling as many assets as they could.
Sakurai: Oh god, these games need to be out by November and all I've done is work on Palutena's custom moves. I have all the models from Uprising on my desktop, I'm putting as many of those guys in as I can. What other 3DS games came out? Dillon something? Put that fucker in there. Cut Ice Climbers I don't have time to deal with this furshading shit.
Mario: Mario is Nintendo's bread and butter. He gets free reign to do whatever he wants. You could make a good Smash game solely with Mario characters. Hell I wouldn't mind it if they put MORE Mario stuff in there. I love that NSMB got a stage BAH BAH. Where's my SMB3 airship level? Look man, Sunshine was a good game, but we don't need Delphino again. Also I would prefer to see more Galaxy stuff. We had two of those games on Wii, yet we get one stage. A stage with GRASS and a HOUSE. Out of all the amazing sights of the Galaxy games, this is what we settle on?
Yoshi: You got Yoshi and basically a new stage every game. I'd like to see more songs, but I'm not really sure what else you can really add. A Shy Guy assist trophy? Some huge ass egg item?
DK: Honestly I'm not a huge DK fan, but I do agree that he is very underrepresented. I wanna ride Rambi! 75m is a fun concept for a stage, but not good to fight on. Just make it 25m. All the jungle levels are basically the same, but I like the dual plane one. The songs are redonkulous. If I had to remix Jungle Level over and over again I'd go deaf. Also good god, please let's move past the bongos and give him a good final smash.
Wario: I like the Warioware series, but I like Wario Land even more. It's sad that this part of him is basically completely ignored. They even took away his shoulder barge. His Wii game had a great visual style so I would have like to have seen that represented in some way. Or maybe a stage based on Wario Land 3, HIS BEST GAME.
Zelda: No new characters in 14 years. No, Toon Link doesn't count. Ganondorf is forever a Falcon clone. I don't care if they kinda turned him into the One Punch Man, he's still too cloney. There are numerous candidates: Pig Ganon, Wind Waker Ganon, Impa, Tingle, Skull Kid, Vaati, Zant, Demise, Ghirahim, Fi etc. Zelda is another series that could easily fill up a fighting game roster alone. I think the song selection is pretty great, but nearly every level is like the plains or a castle. Where was the Link's Awakening stage on the 3DS version? I want to fight with the big egg in the background. HOW DID THAT NOT HAPPEN?
Metroid: The stages need more variety, but I think the representation is pretty good. I mean who else are you going to add? Dark Samus is seriously the only good contender. I want Ridley as much as the next guy, but it's not going to happen. At least his boss fight stage is cool.
Kirby: Kirby was Sakurai's baby before Dark Pit corrupted him and HAL developed the first two games by themselves, so he also kind of gets free reign. Kirby has a ton of games so there's always more things you can pull from. I really like how his 3DS stage is a big homage to the Game Boy.
Pokemon: Pokemon is one of Nintendo's biggest franchises, so obviously they should get a lot of inclusions. Hell, there are so many Pokemon you could put in the game that Namco is making their own Pokemon fighting game. The stages are pretty diverse and interesting, plus the Pokeball item is one of the best in the series. My main gripe is that there isn't a single Gold/Silver song in the Wii U version. All other gens have a song, WHY DO YOU HATE JOHTO SAKURAI?
Star Fox: I'd prefer Wolf over Falco, but I think it has good series representation. Pretty sick of the Landmaster though.
Fire Emblem: Awakening actually sold copies, so you can't fault them for featuring it heavily. Four fighters is actually quite a bit, even though there's a lot to pull from. Keep in mind that the US didn't get any FE games until the GBA, and there were even DS titles that didn't make it over here. Two of the three stages are kind of based on nothing though, just an amalgam of stuff from other games. I'd like to see the stages focus on specific moments in the series.
Kid Icarus: Good god. Look, I know why there's so much representation. It's easy to take assets from and Sakurai worked on it. So many damn enemies in Smash Run are ugly KIU jobbers. Also why does KIU get TWO assist trophies? They took out Isaac for Phosphora? ISAAAAAC. The Palutena's Guidance segments are really funny though.
Earthbound: I know a lot of people complain about how the Mother series gets dumped on and people are mad about Lucas, but Earthbound has more inclusions than I expected. The 3DS version has a stage based on the original Mother, talk about going retro. We also have numerous items and assist trophies. I would like to see an original Wii U stage though, I mean we got two in Melee.
F-Zero: Everything was Mute City. Sakurai pays more attention to this series than Nintendo does, so consider yourself lucky.
Pikmin: There are Pikmin, what more needs to be said? Alph could be his own character if they gave him different types of Pikmin than Olimar I suppose. I'd like to see a giant Duracell battery item.
Animal Crossing: I think this series is actually pretty underutilized. First of all, the game is completely based around items. In Smash you just have the pitfall and the beehive, literally the two worst things in AC. Also Smashville and Town and City LOOK EXACTLY THE SAME. At least make it a different season or something. The song selection is great and there's a lot more you could add. You can certainly add in some more characters as well: Isabelle, Tom Nook, KK Slider, and even New Leaf Villager (completely different design from the current Villager which is based on City Folk). Also bring back Mr. Resetti as an assist trophy.
Other dudes: Shulk, Little Mac, Game and Watch, Duck Hunt, Wii Fit Trainer etc. are all ok. The third party characters are lucky to be in here so there shouldn't be any complaining about those guys.
I definitely think some franchises could have more, namely Golden Sun. There is ONE Golden Sun song between the two games. Not even an Isaac trophy. That's cold.