kkJohn, and easy.
Reason why T-3000 wins.
Dude is crazy strong.
John has phase metal allows for a T-1000 like regen, but in general more sturdy, and harder to damage than liquid metal.
John has shown two ways to attack.
As stated, John is made of Phase Metal. Its is self replicating metal for regen, but can break down to form around attacks, obstacles, or to use in attacks.
Add in John being a super smart human, and insanely skilled in a fight against overwhelming odds, I am not seeing how he loses.