My problem with Lucina, Dr. Mario, and Dark Pit is that while they share their moves many animations and attacks with their base, they aren't as well-made and thought out as Melee Falco or Melee Ganondorf. Those 2, despite being very cloney in Melee, felt completely different from Fox and Captain Falcon, respectively. Their attacks sent at different angles, some moves that were useless for Fox and Captain Falcon were now useful for them and vice versa for their bases, some special attacks (Fox's Blaster, Captain Falcon's Falcon Dive) were made wholly different in function for them, and all around they had a lot of thought put into them despite sharing so many moves.
Lucina has been looked into for further inspection. When Sakurai initially unveiled her, he said that she's very similar to Marth, but has power throughout the sword, meaning she has no tipper. As it turns out, now that the game's out, we know that this is literally the only significant difference she has. Sure, her air speed is faster, but that's it. She was so shoehorned in without any real thought other than "She's popular in Japan, and Americans like her too, so let's put her in SOMEWHERE," that it makes her nearly redundant. Her attacks don't even launch at different angles, they act the same as all of Marth's attacks, just without a tipper. I hate this because I like Lucina as a character, she deserved better.
Dr. Mario is buffed Mario again. He was probably included for fans of Melee Mario's moveset, but Sakurai probably still doesn't know that F.L.U.D.D. is still an almost useless move while Dr. Tornado will always have a good use. Dr. Mario's fair still sends opponents upwards, so unlike regular Smash 4 Mario's fair he doesn't need to use it near ledges to KO and can use it anywhere he wants. His Megavitamins are still a more useful projectile because of their better trajectory and that they harass opponents better, making regular Mario's fireballs seem useless by comparison. And his throws are much better save d-throw, which Mario now has over Dr. Mario. Really, all these changes could have been done to regular Mario to make him a better character, because as it stands when comparing the two, Dr. Mario is always gonna be more useful. Thanks to Sakurai's careless reimplementation of him from Melee, he became the version of Mario that makes the other look obsolete once again, and I hate that.
Dark Pit made a lot of people mad. For them, he was the final straw. Not for me, I despise Dr. Mario more than the other 2 clones, who I'm more disappointed with rather than angry at, and it confuses me that more people are mad at him than Dr. Mario, but I digress. For them, it gave Kid Icarus one character too many. Or at least, the decision to add him but not a Donkey Kong, Metroid, or F-Zero character as well left a sour taste in many a fan's mouth. I personally was willing to look past Dark Pit's inclusion if he looked well-done, especially since he could use different weapons from Pit because Uprising had lots of different weapon classes, and because I like Pit's moveset and looked forward to how they could tinker with it for a clone, but he didn't. He still uses a bow for all his normal attacks like Pit does, his special attacks have very little differences from Pit's (only his side-B seems to send at a different angle), and although he holds the Dark Pit Staff in his artwork, he only ever uses it for his Final Smash, acting like Zelda or Sheik's Light Arrow. That's some real Melee Ganondorf artwork crap, which also had him holding a weapon but never using it. Looking at the footage, it makes me sad that his situation is similar to Dr. Mario's in that he looks like a mostly buffed Pit made into a separate character, making the original Pit look almost worhless in comparison, because unlike Dr. Mario he's a different person from Pit, not Pit wearing different clothes. Yes, his character design LOOKS like Pit with dyed hair and wings, but unlike Dr. Mario it's made clear in his game that he's someone else, not just Pit after a trip to the beauty salon. All in all, a giant missed opportunity.
Again, I reiterate that while the OP of this thread used Falco as an example, his case isn't the same because his inclusion had thought put into it, even if he was included last minute, because Sakurai still modified him to be a worthwhile counterpart to Fox--as any Melee / Project M fan will tell ya. These are all filler, and I don't like it.
Edit: No, I don't believe any of these "got in" over anyone else. My disappointment comes from how they all could have been so much more, but aren't.