Willie is annoying, but also attractive, funny, and feminine, so it’s endearing. Steven Spielberg certainly didn’t think she was unlikeable. Indy, just like the audience, thinks she’s annoying but attractive too, so we identify with his interactions with her. Elsa is seductive and charismatic--and evil, but those qualities are not mutually exclusive. Before the audience and Indy know she's evil, she's unreservedly attractive. Inevitably afterwards still, too, which gives it some edge.
Wombat, meanwhile, is unlikeable, unattractive, smug, and sociopathic. She exists to undermine Indy and talk about how great she is. A perfect character for delusional social pariahs on Twitter to identify with, but not everyone else.