Personally, I'd like to see the MK team pull a "Twisted Metal" and revamp the stories and characters. TM has a history of keeping the same characters but changing them either appearance-wise or storywise throughout the games. TM: Black was a great example.
Since the next MK is going to be on next gen, I wouldn't mind seeing a total reboot with some of the more iconic characters and some new characters (or characters of the same race but with different backgrounds aka a new Tarkatan or Lin Kuei)
For the next MK (if it was a reboot) I'd like MK to return to the darker, Asian-mythology elements of MK2 with characters to represent that...
*Obviously with a reboot not everyone can make the cut so I picked my own iconic characters and a few other character choices to make things interesting
Returning Characters
Kung Lao
Liu Kang
Sonya Blade
Jax
Kenshi
Kitana
Raiden
Sub-Zero
Scorpion
Quan-Chi
Kano
Mileena
Reptile
New Character Ideas
A New Earthrealm hero (introduces a Muay Thai fighter)
An Outworld ronin (possible Kenshi rival)
A New Tarkatan
New Lin Kuei (“Okami”, Lin Kuei who can turn into a werewolf)
Evil Sumo
Tengu Assassin (a warrior of the Tengu Clan possessed by a demon)