-No Snake, Mewtwo or Ice Climbers. I actually feel like Dark Pit, Lucina, and Dr. Mario were put into the game because something didn't work out with those three characters, so they made 3 clones to make up for it.
-Lack of original 3DS stages. Pikmin, Punch Out, Star Fox and Xenoblade make sense as they don't have many handheld titles. But why do Warioware, Mega Man, Donkey Kong, Yoshi, and Metroid have to rely on past stages? They all have had quite a few hand held games, it confuses me even more as Mario, Pokemon, and Zelda managed to get multiple stages.
-Lack of an adventure mode although the Wii U version might have one.