In Twelfth Night, Viola is the heroine, yet she is an instance of the heroine being a hero as well (e.g.; Hero in Much Ado About Nothing and Rosalind in As You Like It). As such, Viola's character is predominantly comprised of good qualities. Viola's good qualities range from sound judgment, honesty, loyalty and intelligence to charm and emotional stability.
It is Viola's sound judgment that enables her to rightly evaluate the sea captain and to know he was trustworthy. It is her honesty and loyalty that lead her to loyally represent the Duke's love suit to Olivia even though she has fallen in love with the Duke herself. It is her intelligence and charm that lead both the Duke and Olivia to love her and trust her. It is her emotional stability that keeps her level-headed despite the Duke's depressive melancholy and Olivia's extreme emotionalism.
In addition, Viola's intelligence and charm show themselves to great advantage in her sparkling, interesting conversation and musical talents. Her intelligence is also highlighted in her witty word-play asides to the audience.
Her most prominent bad qualities are, ironically, the same sound judgment and intelligence that makes her so admirable. These have blind spot to them since Viola is unable to apply them in matters of the heart. Possessing sound judgment and intelligence, she nonetheless falls for a less than admirable and emotionally rocky but handsome Duke. The only thing the Duke's qualities will mesh with are Viola's charm; musical and canversational talents; and loyalty.