In the sequel, the Big Bad
will be her rival.
Salt is likely not the only agent who's considered the best. There's probably another agent who's trained just as much as Salt did. She might also be a chick. And the two don't really like each other.
Also, one of the agents at the secret base in the first movie must have survived Salt's onslaught. He sent a message to other sleeper agents everywhere of Salt's betrayal. The Rival
sees this as an opportunity to fight her in an ultimate showdown. During the fight, just when she beats Salt she'll hit her Berserk Button
(Mike's death), which will be her own downfall.
The sequel shall be named as "Pepper"
Get it? Salt? Pepper?
The program also involved cybernetic/biological enhancements
Why can she jump onto cars, survive ridiculous falls, and beat the shit out of everyone? Because the Russians didn't just train their minds, they also modified their bodies.