Pallete Swapping - Something relatively small but I would love to see multicolored Yoshis in Mario Kart 3DS's multiplayer or Online mode. Also, instead of having 3 Mario's in one race, why not have a Fire Mario, regular Mario and Cloud Mario in one race. Maybe Pallete swapping for karts too.
Removal of Snaking - Yes; not everyone snakes, but it punishes those who choose not to do it and gives those who do choose to snake, an unfair advantage in time trials and multiplayer races.
Return of Mission Mode - Quite possibly the best new feature in Mario Kart DS, I'd love a reappearance in its successor.
A new Wi-Fi ranking system - The Wii format doesn't work well for those are just plain unlucky. I know from experience that it sucks to lose 400 VP from one race because you didn't have red shell fodder or you're hit by a Spiny Shell in the last lap and the finish line is right in front of you. Especially when you're only getting 15-20 VP from getting first in races with less experienced players. Also the DS format doesn't work because it encourages disconnecting/ragequitting and it doesn't make immediate success worth while because you have to win 1st in an entire GP or get a lose/disconnect.
Rebalancing of Drifting - In Mario Kart Wii, inward drifting is incredibly broken. I really don't know how they could rebalance it but maybe buff the mini-boosts for outward drifting vechiles and nerf the mini-boost of inward drifting vehicles.
Bikes and Karts - pretty self explanatory.
Miis Playable - once again self explanatory.
Optional Team based Battle Mode - Yet again fairly self explanatory.
Meh, If none of these appear in Mario Kart 3DS I'm sure I'm still going lose hundreds of hours playing it.
Pixel Art can be fun.