IMO it seems like they were both equally popular but Sub-Zero kinda lost a little popularity with the unmasking (even though the people of MK have smoothed that whole messy situation with the OG Sub-Zero becoming Noob Saibot, and Kuai Liang etc etc), which I personally didn't really have a problem with, once you realize his gameplay wasn't compromised (that 6 hit combo he had that involved all the punch/kick buttons, and that fatality where he raises you up, freezes you and breaks you in half
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).
Also, once Mortal Kombat went into 3D, especially after Deadly Alliance, Sub-Zero became more of a slow, bruiser type of fighter while Scorpion has some speed to his fighting, and of course the casual gamer is gonna wanna lean more to the faster character, not to mention Boon being a Scorp fan.
Then again, Scorpion has one main thing, which Sub-Zero does not, which is...
I'm more of a Liu Kang guy (Liu had the juice from MK1-3 no question), but I like Sub and Scorp, they were both great in UMK3.