(This is a long post so I put the character names in bold for anyone who just wants to skim to a character they may want to read about.)
First things first, Sakurai didn't need to pad the roster with clones because at this point it is already extremely robust. Dark Pit, Lucina, and Dr. Mario could and should have been alts. I would have been perfectly fine with that. He could have fit more characters by going the Bowser Jr. route. Even with that, I'd probably still buy DLC characters.
The set of newcomers in this game is much better than Brawl's. They're more varied and more importantly, seem like a lot more fun to use. Brawl's newcomers were mostly obvious choices despite surprises like ROB. It's a bit strange that it took three games to include Wario and Diddy Kong. I was excited when they were announced then not terribly satisfied when I got to play as them. I was particularly let down by Wario who, even in the 3DS game, doesn't have his shoulder charge (not sure if that's a custom move). Not counting how lame the additions of Dark Pit and Lucina (though I prefer using her over Marth) are, the worst newcomer for me is Greninja, and he's still pretty good.
Wii Fit Trainer is a beast. I still fail at Deep Breathing sometimes, but I'm getting better at it.
I'm still not familiar with Shulk's Monado Arts. I like him, but he'll take some getting used to before I'm anywhere near competitive with him.
I'm glad Palutena is in the game. I'm still working out a strategy with her. I'm having trouble hitting her forward Smash move. I end up just slightly blowing away my opponents with her wings instead of devastating them with pain and suffering.
I think I may actually like Pac-Man more than Mega Man. It seems like a total waste that Mrs. Pac-Man isn't a Pac-Man alt.
Rosalina and Luma are absurdly strong. I haven't spent too much time with them, but I was doing pretty well despite not really having a working knowledge of their moveset.
Additionally, Smash 3DS improves most of the returning characters. King Dedede is still just not very fun to use.
Pit got buffed. He was good at racking up damage in Brawl then absolutely awful at getting KOs. Here, they took away his cheapest move ("Hiyayayahh") and gave his Smash moves more power.
Mario is vastly improved. This is the most fun I've had using him though I haven't really picked him since N64 when there were only 12 characters. The demo kind of forced me to try him and I'm glad I did. I'm still having some trouble hitting his forward attack in the air. And yes, FLUDD is downright useless. The cape is useful in very specific situations beyond just countering projectiles. For example, if Little Mac does that lunging punch, use the cape to turn him around and if he's near an edge, he can't recover.
Link was so amazing in Melee then just not very good in Brawl. Here, they've struck a good balance. Toon Link absolutely deserves a roster spot yet is still a completely wasted opportunity. For a series as important as The Legend of Zelda, it's pretty inexcusable to have two characters still be clones.
Peach is definitely faster now, possibly the fastest she's ever been even by Melee standards. She was awesome in Melee then nerfed to all hell in Brawl. I haven't spent too much time with her. I definitely can't spam turnips as egregiously now. I'm still upset that despite some minor alterations to her moves, none of them take cues from Super Princess Peach. Her final Smash is still awful.
I've definitely put the most time into playing as Busty Samus. She's awesome in this game because of her rocket boots. Her forward Smash move is far improved. In fact, her everything is improved because she was flat out fucking awful in Brawl.
I'll comment more on other characters later as I've spent a lot of time going back and forth between playing a certain character then writing short blurbs about them.