I may get some flak for this, but I'm gonna be blunt ant to the point: The game's presentation of itself and it's content.
I was (foolishly) really hoping the 3DS version of the game would be extremely fleshed out to really stand out on it's own as a fully-fledged game with an abundance of content and modes and things to do, but considering that aside from Smash Run, most of the stuff in this version is also going to be in the Wii u version or can be transferred over to it, I've slowly been noticing how little of it's own stuff it actually has. That includes the stages too, a large abundance of which are simply from previous games it seems or might be in the Wii U version in some cases. I mean, the stages that are new and exclusive to the 3DS version all do look good for the most part, but...I dunno. When it comes to everything, even Classic Mode and All-Star, I can't help but feel like this game is either incomplete or just doesn't have much to it and the Wii U version actually is where the big meat of the Smash experience will be at. It really feels like 3DS Smash is just "get coins, get trophies, get custom moves for the Wii U version early".
tl;dr: 3DS Smash literally feels like it's just "Smash 4 Lite". I find it even more ridiculous that Sakurai wanted us to think of 3DS and Wii U as the 4th and 5th entries in the series when the 3DS version is really just a smaller version of the bigger one.
Not to say that there's anything inherently wrong with the 3DS version, though. It still has a lot of charm. It vastly surpasses Melee and Brawl for me in terms of how it pulls me in and keeps me interested. I just feel like there's so much more we aren't being given yet, which goes without saying since the Wii U version isn't out yet.
Still, good game. Definitely like it. Even if I'm not at all happy with the unlockable characters, which is another part of why I find it lacking.