I just need to say this...
I think we'd all be a lot more pleased with the roster if we try to stop thinking of it in terms of which series "deserves" more reps than another, coming up with arbitrary numbers of reps that each series "should" have, etc. Now, this is coming from someone who lists Ridley and King K. Rool as two of his most wanted newcomers. I'd definitely be disappointed at their exclusion. At the same time, the current roster is fantastic, and I'm certainly not going to blame either of those characters' exclusion on something like Dark Pit.
I really don't think "bias" is the correct word. As for items and Smash Run enemies, it is true that Uprising received more content "than it should". At the same time, none of that content is forced. In my opinion, none of it looks like something that shouldn't be in Smash, but Sakurai shoehorned it in anyway. Around here, we seem to like to count things; playable characters, items, ATs, Smash Run enemies... and then enrage ourselves over these numbers. I think that's completely backwards. Instead of setting down an arbitrary number and saying "_____ series CANNOT exceed this many Smash Run enemies", I believe Sakurai is only trying to make the game as engaging as possible, and his experience with Uprising produced many things that just fit in Smash. He's even said that he was thinking of Smash while making Uprising. My final point on items and Smash Run enemies is that many people won't even deal with them due to disabling items and not playing Smash Run extensively, but when we DO use items or that mode, no sane person is going to be concentrating more on which series each item/enemy is from as opposed to just enjoying the game. It's really, truly not a big deal.
Playable characters are a bigger deal, but people are still getting themselves worked up too much. It seems that the mere existence of Dark Pit on the roster has triggered many to obsess over the fact that "Kid Icarus has 3 characters and DK and Metroid don't". But there are many issues with that statement, the largest being, in my opinion, that Dark Pit is likely a clone. The most likely reason for his inclusion is the most likely reason for Lucina and Dr. Mario: they were supposed to be alts that were promoted to playable characters, either due to small gameplay differences or to pad the roster. As much as I want Ridley, K. Rool, Mewtwo, Isaac, I'm not foolish enough to think all or any of them would be in but for the existence of Dark Pit. I just don't think that's realistic.
Finally, I'd like to address the "better choices for clones" argument. If we honestly step back and consider the entirety of the process, I have to say that Dark Pit is probably one of the "best" choices for a clone Sakurai could have made. Let's start by listing Nintendo characters that are similar enough in body structure to a current member of the roster to feasibly be made into an alt/clone, and who are also characters one could at least envision in Smash:
Dr. Mario
Dark Pit
Lucina
Dixie Kong
Dark Samus
Daisy
Shadow Link
Toon Zelda
Impa
Lucas
Wolf
There are probably more, but I think the above list is pretty good. Now, let's think a little deeper. Which of the above characters could actually be a clone in Smash while still respecting the character's source material? In my opinion, this narrows the list to
Dr. Mario
Dark Pit
Lucina
Shadow Link
Toon Zelda
Dixie Kong being a clone of Diddy just wouldn't sit right in my opinion; the amount of changes from Diddy needed to respect her abilities would exceed the changes made to Wolf from Fox. Dark Samus canonically shares basically no abilities with Samus. Further, Smash already has two Samuses; even though Dark Samus is a completely different entity, I think this would be a fact lost on non-Metroid fans who would see only that there are three characters on the roster with "Samus" in their name. Is this a good reason to not be included? Not entirely, but if we were discussing it in the context of Dark Samus being a clone of Samus, I think it would in fact be a deal breaker. Daisy playing like Peach would make absolutely zero sense to me, as Peach's moveset draws heavy inspiration from multiple appearances and unique abilities... floating, turnips, Toad meat shield, none of that would make sense. As for Impa, as often as we see people say she could replace Sheik or be a clone of Sheik, I just don't see it. I feel like that line of thought has more to do with wanting a Zelda newcomer and looking to Impa as one of the few important recurring characters outside of the Triforce holders in the Zelda series. I just don't get the feeling that Impa as a clone of Sheik would be well-received, especially given the recent uniqueness given to Impa in Hyrule Warriors (which, yes, is a (non-canon?) spin-off, but I still think that being a clone of Sheik in Smash would be entirely underwhelming given that iteration of Impa). Lucas and Wolf, finally, probably could work as clones of Ness and Fox respectively. Their issue, ironically enough, is being fairly unique vets from Brawl. People would be outraged, I believe, if Lucas and Wolf were actually made clone-ier for Smash 4 just for the sake of getting them on the roster. I could definitely see them being cut for this reason; if neither were in Brawl, I think very few people would scoff at the idea of Mother and StarFox "only" having 1 and 2 reps, respectively. I think Sakurai may have taken this into account when deciding the roster; that Ness and Fox/Falco represent their series very well already, and Lucas and Wolf aren't really... necessary, I guess. They're unique enough to take more work than a normal clone to implement, but at the same time taking their uniqueness away just wouldn't feel right.
Now to finish narrowing the list. Shadow Link is unnecessary. For the most part, Shadow Link has been an entity totally unimportant to the story of Zelda, and serves as a random boss. He also has the same issue as Dark Samus, being that we have two Links on the roster already, and a third is just too much (I see it as the same issue of the 3 Landmasters from Brawl, but on a larger scale since we're talking about entire characters). Toon Zelda is workable I suppose, but with the potential for transforming into something like Tetra gone (with the mechanic removed from Smash 4), I don't feel that she has much going for her. Not to mention that I think Toon Link is already pushing it, and to have TWO toonified clones from the same series would be somewhat irritating.
Now let's look at Dark Pit. He's a mirror of Pit who possesses the same abilities as Pit, and so to see them fighting similarly is not weird at all. He's also completely his own character which, in my opinion, puts him above Mario-in-a-doctor's-outfit. Finally, he would be exceedingly easy to make starting from Pit, so he would require quite a small investment of resources. In fact, of the clones we look to be getting, Dr. Mario would get me upset LONG before Dark Pit would.
I think these are things we should all take into consideration before getting upset over "overrepresentation" of Kid Icarus, or (basically) equivalently, underrepresentation of franchises such as DK and Metroid. I'd be very happy to see both of those series receive more love... I just really, honestly don't feel that it was a situation where KI is the reason they're not receiving as much, where Sakurai sat down and decided "more KI, less DK". To close, yes, we can compare representation between series... but as I said above, I don't believe it's anywhere near as simple as just comparing sales data or popularity polls. Much more goes into the decision for content in Smash, and I think appreciating that fact can go a long way to appreciating Smash 4 for what it is.