It's looking to be Johnny & Sonya, followed by Cassie & Takeda.

However, one of the big ways I think MKX's Story differs from MK9's is its intertwining storylines; things don't seem to boil down to a single idea, I.E. Shao Khan. For this reason, I expect we'll be introduced to different "core" characters depending on which storyline is being addressed (From Shinnok, onto Quan Chi, onto Mileena, onto Kotal's rule, to Shinnok's return, etc...)

I'm thinking the group of Cassie, Jacqui, Takeda, and Kung Jin are going to have a lot of story time devoted to them. The story does time jump several times, but I remember an interview some where that most of the story takes place 25 years in the future from Shinnok's invasion.

I would say the new generation characters, since that's the whole theme of this game. That was also alluded to in the story trailer.

Main Heros
Cassie
Jacqui
Takeda
Kung Jin

Supporting heros for star power
Raiden
Sonya
Johnny
Kenshi

Does anyone sense some GI Joe in the new SF of Cassie's team?

Teen titans.

Blue Kano is my hero.

There will be different heroes for different chapters

Neatherrealm war
Johnny Cage

Outworld war
Kotal Kahn

Final arch
One of the SF members

It looks like Cassie is going to be our first female 'main' hero, which I think is really exciting.

The other 3 descendents are her sidekicks, with Takeda as the Kung Lao sort of right hand man.

The Netherkast guys were saying they think Scorpion could act as one of the main heros in this one as well. Very possible.

Cassie has been shown off a lot, so I would give the primary protagonist position to her. Takeda and Kotal also seem prominent in the comic, so I would put them up there as well. To me, Johnny will be a main character for the first part only, and hand off the reigns for his daughter to take over.

I would love for it to be Cassie - she's not everyone's cup of tea, but I think she's an awesome character, and having a girl be the champion for once would be something new for MK.