Are the three couples really well matched, or is Shakespeare's point really to assert the arbitrariness of love? Two disadvantages can be seen in the pairing of two out of three couples, while only one match is advantageous.
For one thing, one reason why Olivia seems to have fallen for Viola as Cesario is because Cesario is sensible while Olivia is certainly not. The very fact that she has decided to allow herself to grieve over her brother's death for seven years shows us just how emotionally driven and lacking in sense she is. She even shows a lack of sense with respect to her rejection of Duke Orsino whom she knows to have a noble and virtuous character. Hence, when Cesario shows up in her home and criticizes her, even calling her the "cruell'st she alive" for rejecting Orsino and planning to leave "no copy" of herself, meaning offspring, Cesario is really pointing out just how much Olivia is lacking in sense (I.v.225-27). Cesario even asserts that she finds "no sense" in Olivia's rejection of Orsino when his love is so intense (251). Since Viola as Cesario sees just how nonsensical Olivia is being, it shows us that Viola certainly has more sense than Olivia. Sebastian, on the other hand, more like Olivia rather than his sister also proves to be very emotionally driven. We see evidence of this when he rejects Antonio's company simply because he is grieving over what he thinks has been his sister's death. We further see it in his violent reaction to Sirs Toby and Andrew. Is it really wise to pair two emotionally driven individuals who lack sense? In terms of character, Viola as Cesario would have been the better match, but of course the one advantage Sebastian has over Viola as a match for Olivia is that, of course, Sebastian is a man.
The other ill-matched couple in the play is Sir Toby and Maria. Maria knows Sir Toby to be of bawdy character and openly criticizes his excessive drinking habits. But while we see Maria criticizing his wild, untamed character traits, it is she who comes up with the prank to play on Malvolio. So would it really be wise to pair a man with a woman who ultimately would only encourage his wild and uncontrolled behavior, even though she also criticizes such behavior? What's worse is that even though Maria thought of the prank, it was Sir Toby who came up with the idea to have Malvolio locked up in total darkness as a madman, proving just what a poor influence Maria would ultimately have on Sir Toby's character.
The only couple that really makes sense is Viola and Orsino. Viola has enough sense to temper Orsino's irrational emotionalism. More importantly, Viola is genuinely devoted to him and loves and respects him for his noble character, plus has already served him out of friendship.
The fact that Shakespeare poorly matched two out of three couples helps show us that his real point is to assert both the arbitrariness and foolishness of love, which are central themes in the play.