With the rumor of MK v SF going on again, I spent some time coming up with how I would imagine things would go down...

Story
When the merging of the two universes begins, people and events are drastically altered. Only Raiden, a god who is immune to the effects of the merger, can see the difference. Scorpion, being a wraith, is able to see the differences too. He witnesses these events firsthand when he confronts his former enemy Sub-Zero, only to be greeted with a friendly sparring match. Sub-Zero believes they were friends before Scorpion was murdered in cold blood, and Sub-Zero has spent his time wandering Earthrealm, searching for the one responsible. When Raiden sets out to undue the merging of the realms, his intervention only leads to conflict between the various fighters. But when the merging is undone and people's lives return to normal, Bison sets his eyes on the fighters of the Mortal Kombat tournaments. Seeking to build an army of unstoppable warriors, the Mortal Kombat universe is the ultimate source...

Cover Image
Sub-Zero & Scorpion Versus Ryu & Ken

...Why? These four are the most iconic characters and the original palette swaps of their respective series. I think they would embody the longstanding rivalry.

Cast
Taken from MK2 and SF2 timelines when these series hit a peak

Raiden
Sub-Zero
Scorpion
Liu Kang
Jax
Sonya
Kung Lao
Johnny Cage
Shang Tsung
Kano
Kitana
Mileena
Baraka
Reptile

Ryu
Ken
Chun-Li
Guile
Cammy
Sagat
E. Honda
Dhalism
Fei-Long
Blanka
Vega
Zangief
Bison
Akuma
*Notable absentees are T. Hawk, Balrog and Dee Jay

Story Changes
*These would be reverted back to normal halfway through Story Mode
Sub-Zero claims Scorpion and he were once friends and training partners (Ryu and Ken's story)
Guile is the leader of the US Special Forces (Jax's story)
Liu Kang has taken an alternate path to become a movie star (Fei-Long's story)
Kano is a member of Bison's Shadaloo organization (Zangief's story)
Sagat seeks vengeance on the monk Kung Lao, who scarred him in their last battle (Ryu's story)
Kitana was brainwashed by the Shadaloo organization (Cammy's story)
Johnny Cage has become a US martial arts champion thanks to Ryu (Ken's story)

Potential Story Mode Rivalries

Sub-Zero V Ryu
Two lone warriors who prefer isolation and strive to better themselves

Scorpion V Akuma
Two hate-fuelled warriors with the power of darkness

Raiden V Bison
Two super-charged heavyweights who happen to be polar opposites – Raiden, the protector of the Earth, and Bison, a terrorist wanting conquer the realm

Jax V Guile
Two military meatheads fighting for superiority

Sonya V Chun-Li
A member of the US Special Forces and an Interpol agent investigating the “merging”

Liu Kang V Fei-Long
Both of them use fiery attacks and embody the traits of Bruce Lee

Johnny Cage V Ken
Two martial artists whose cockiness would definitely lead them to bump heads

Kitana V Cammy
Two beauties that have a similar outfit and are both deadly assassins

Mileena V E. Honda
A seductive but savage assassin is opposite to the Sumo's code of honour and pride

Kano V Zangief
Two powerhouses who rely on brute strength and are both criminals

Kung Lao V Sagat
Two great fighters who live in the shadows of their rivals and seek to redeem themselves

Baraka V Blanka
These two are the savage beasts of their respective series

Reptile V Vega
Both of them are two stealthy assassin-like warriors who use claws in battle

Shang Tsung V Dhalism
The evil sorcerer's dark magic versus the wise Yogi's mystic powers

***

Other Matchups

Liu Kang V Ryu
Two of the best fighters going head-to-head with fireballs and crazy kicks

Cage V Zangief
Both Cage and Zangief have been the comic relief of their series

Mileena V Cammy
Similar reason to Kitana and Cammy's rivalry (all of them are beautiful assassins)

Baraka V Vega
It would be fun to see their blades clash in a vicious battle

****

Potential Crossover Tag-Teams

Scorpion & Akuma, “Demon Alliance”
Enemies at first, but form an uneasy alliance up to destroy their enemies Sub-Zero and Ryu

Cage & Fei-Long, “Double Strike! Action Superstars”
Two martial arts action movie stars that team up on the big screen

Sonya & Cammy, “Special Agent Tag-Team”
Two blondes with similar training and fighting techniques would make a great team

Shang Tsung & Bison, “Pyscho-Sorcery”
Two power-hungry forces who enslave the souls of great warriors to serve them

Who do I think would honestly win in these battles?

* = WINNER

Sub-Zero V Ryu* (Ryu's training and power of drive to never lose gives him the advantage)
Scorpion* V Akuma (Scorpion's rage and wraith-like powers give him the advantage)
Raiden* V Bison (Raiden's godlike power gives him the advantage)
Jax* V Guile (Jax's brute strength gives him the advantage)
Sonya* V Chun-Li (Sonya's Special Forces training and survival instincts gives her the advantage)
Liu Kang* V Fei-Long (Liu Kang's powers and training gives him the advantage)
Johnny Cage V Ken* (Ken's training and power of attacks gives him the advantage)
Kitana V Cammy* (Cammy's strength, training and agility gives her the advantage)
Mileena* V E. Honda (Mileena's sais and savagery gives her the advantage)
Kano* V Zangief (Kano's cutthroat attitude and knives gives him the advantage)
Kung Lao V Sagat* (Sagat's Muay Thai training and drive to win gives him the advantage)
Baraka* V Blanka (Baraka's blades and his bloody ferocity gives him the advantage)
Reptile* V Vega (Reptile's stealth and acidic capabilities gives him the advantage)
Shang Tsung* V Dhalism (Shang Tsung's number of souls and dark magic gives him the advantage)

MK wins 10-4

I just think the brutality of the MK fighters would be the deciding factor. The MK fighters are just as skilled as the SF fighters, but they will actually KILL them.