I've only ever
really invested time in playing MK Trilogy and Deadly Alliance, but I'm probably safe in assuming there aren't a whole lot more characters to pick from.
Typically I'd go for Scorpion, Shiva, and Reptile. The latter sucked in DA, so I dropped him in favour of Shang Tsung; whose sword skills I was particularly fond of.

In Trilogy I'd commonly go for the above, plus Motaro - he's completely overpowered like the other bosses, but I can't help but
love him for how you can overwhelm your opponent with such diversity (contrary to boss' simplistic 'hit 'em hard' take on fighting).