Gameplay-wise, mainly, which I find it to be very repetitive with the time, and I'd also say the lack of development of some characters (Magnus and Medusa mainly).
Agreed on that Medusa and Magnus get little spotlight.
The single-player levels do get repetitive since they revolve a lot around the story, so playing for a second time isn't as memorable unless you really like particular parts of the story.
Multiplayer is great. Just as great as Smash.
That and KIU's over-representation in Smash 4, especially on 3DS, doesn't help either.
I never got, I still don't get and I probably won't ever get this logic.
It's just ported stuff that was easily tacked into the game. lol
I really don't see what's the big deal with the KIU content in Smash 3DS. By the way, Smash Wii U doesn't nearly have the same content as 3DS being roughly the same as other minor franchises represented in the game with almost no trophies, two stages like most franchises and two Assist Trophies. Before you whine about Palutena's Guidance, do remind that Star Fox also has conversations, just like Melee and Brawl.
Okay, there are 5 items added, but those just happen to work well in Smash because the games are so similar in the first place, so the items are easy to recreate from a design point of view. Ideas that add to the gameplay are always good.
Ah well, to each their own I suppose...