In my opinion, the only games with lacking representation are Donkey Kong and Wario, and it's not because of the numbers game a lot of people are playing. It's because neither of those characters feel like they represent their respective franchises to me.
Donkey Kong and Diddy Kong have realistic monkey noises for...some reason? And every stage they've ever had is just some generic jungle (especially in Brawl, because Rumble Falls is embarrassingly bad). They don't feel like platforming characters and they can't even do some of their classic moves. I can't believe that Donkey Kong is only just now getting his roll attack, but hey, it's something.
Wario is similar. Wario has a really strong history with a ton to pull from: Wario Land, Warioware, all of the spin-off games, and also just the fact that he's evil Mario could provide a lot of potential for mirroring his moveset off of Mario in a fun and interesting way. Instead, he doesn't really feel like he represents any of those things super well. I will say, Wario's stages have been awesome if you're a fan of Warioware, and his moveset definitely has a decent sense of his personality with the bike/bite/fart mechanic. This isn't as egregious of an error as Donkey Kong is, but I still feel like there's a lot that could be done here.
I would put Metroid in third, because Samus doesn't really feel "right" to me, but I don't think it's as bad as many make it seem.
Besides that I think Smash 4 did a really good job with representation and I think a lot of people are way too critical. It's about more than numbers, it's about the attention to detail. Yoshi feels awesome in this game. Luigi finally feels like Luigi and not Green Mario. Bowser was redone in a really cool way. We got a number of new franchises represented in characters and all of them are extremely well done. I'm happy with what we got.
I'm certainly sad that Ice Climbers and Snake were cut, meaning we lost two entire franchises, but for everything that remained, this is a lot of solid representation. I think a lot of people have to understand the process of game development and Sakurai's design philosophies before you throw out so many suggestions that don't make a whole lot of sense.
First and foremost, Sakurai wants playable characters included. Next comes the "big bads," and these are typically people that are enemies through out the franchise; one-offs are lame. Third-parties get only the face of their franchise and an assist trophy. There are a few exceptions to this rule, like Pokemon and Fire Emblem since they have entirely new casts in each game, but I really like the balance Sakurai has with adding one or two new reps from each into every new Smash game. Overall I think it's a logical and respectable system for choosing representation.
Outside of that, most character suggestions just don't make sense to me. Mario's reps are all of the playable characters and major bosses through-out the series, bar Toad. These are faces that any fans will recognize. Zelda's reps are all based around the Triforce and I don't see any other new characters as likely. Metroid only has Samus as a playable character, so they focused on her. For bad guys, Ridley's really the only option as far as consistency goes (maybe Dark Samus for Metroid Prime), but if Sakurai doesn't think he works very well than I'd trust him long before any forum dwellers.
DK definitely has a lot of room to grow, both for playable characters and villains. Sadly, they all come from the Rare era, which may be why Sakurai's not so quick to include more. Wario doesn't really have any stand-outs (a lot of people seem to love Ashely, but in game she's just like everyone else). Punch-Out includes the only playable characters (with Doc commentary!) and has no major villain they could use to represent the other side(again, people seem to like King Hippo, but there's nothing in game that marks him as special). Same with F-Zero. Yoshi could include Kamek, but everyone else is totally fine to me.
In terms of representation, I think they have a bit to fix for Wario, Metroid, and DK first and foremost. They also need to bring Wolf and Lucas back. I wouldn't mind costumes for Young Link, Roy, Pichu, and the rest of the Pikmin captains and, while I understand why they were cut, I would like to see Ice Climbers and Snake back.
I also think they could handle adding some more diverse stage representation to the Mario franchise (maybe Captain toad or Mario & Luigi; please no more 1-1 rip-offs) and Pig Ganon to Zelda (to have 2 reps for each Triforce segment). Hell, even Bandana Dee has been playable lately, so throw him in; he makes more sense that Tingle to me. But outside of that, I think most of the franchises currently in the game have just the right characters playable and stages selected.
But overall, going forward, what I want more than anything is more one-offs. Not every franchise needs thorough representation, that just feels forced and, I think, brings down the integrity of the series (especially with all of the ridiculous third party recommendations). I'd like to see a Golden Sun rep, Advanced Wars, Codename STEAM, Splatoon, Panel de pon, Rhythm Heaven, etc. WAY before some lame characters who only appeal to big fans of one franchise. Also, more than anything, I'd like to see gameplay decisions trump any representation decisions. Nintendo characters are great inspiration for fighting designs, but focusing too much on the representation aspect is what made Brawl feel so weak next to Melee for most people.
But tl;dr: I'm pretty happy with series representation in Smash 4. Sorry I wrote so much I didn't realize how badly I was avoiding doing my homework until now.
I sure hope so!