There are a lot of things that can make characters unpopular, take MK9 for example.
Lack of popularity: Nightwolf.
Low on the tier lists: Sheeva.
Hard to use: Shang Tsung.
When it comes to popularity you guys are thinking too small, casuals aren't going to remember one or two appearances on an old show or video game.
Superman and Batman will be like Scorpion and Sub-zero in MK9, super popular in the first month or two, then seen less but still often in the rest of the game career. Unless one of them is broken.
So far everyone seems awesome, I think the ultimate deciding factor in this game will be how good the character is compared to others.
If NRS succeeds in making this game completely balanced with no shit characters or extremely good characters then we might see everyone sort of equally.
And i'm more than sure people will still try out characters they know nothing about, and if they like them they'll probably look them up to learn.
If I had to pick someone though I guess Nightwing, he seems a bit more complicated than most of the cast(like a simplified Gen from SF4), and he isn't super well known outside of the comics(I doubt most casuals will know that he was Robin).