I would say that Frost is undoubtedly the most popular 3D-era character. I can't really think of anyone that could kompete.
Apparently Midway/NRS received a lot of hate mail about Frost back in the Deadly Alliance days, because she was "just female Sub-Zero". She didn't return in Deception, the sequel even though Kenshi, Li Mei, and Bo' Rai Cho did, and she only returned in Armageddon because ALL characters had to. The following for the character has improved a lot, but I don't think she is close to being the most popular 3D character.
Kenshi is for sure the most popular. Kenshi has been in every main MK game since he made his debut, with MK11 being the exception to give him a break. But considering all character appearances and the amount of requests I see, I think some characters like Li Mei and Havik may have bigger followings. If you count MK4, then Quan Chi, Shinnok, Tanya, and Fujin have bigger followings for sure.