The Merchant of Venice is Antonio. Shylock is the financier of Venice. Any alternate title would need to hold true to Shakespeare's original intent of symbolic representation as conveyed by the title. What do we know about Antonio from the play The Merchant of Venice?
We know that Antonio isn't above a little deception to his friends. The information he gives to Salanio and Salarino about his melancholy not being caused by financial woes is contradicted later by what he tells Bassanio, the need for a loan to help Bassanio, and his inability to pay Shylock's demands by the contractually appointed day.
We know that Antonio is devoted to Bassanio and will literally do anything for him, including give up his life to honor a debt. We also know that Antonio isn't above being manipulative of Bassanio while making decisions on his behalf, for instance, when Antonio coerces Bassanio to give up Portia's ring against his will. We also know that he devalues Bassanio's conscience because even though Bassanio protests, Antonio enters into Shylock's immoral and outrageous loan contract agreement.
We further know that despite Antonio's good qualities and in keeping with his bad qualities, he behaves in atrocious manners toward Shylock. Yes, the Medieval and Renaissance age were times when Jews were especially discredited and subject to all manner of restrictive laws, but Shylock doesn't accuse Gentiles of mistreating him, he accuses Antonio of mistreating him: Antonio has a particular animosity against Shylock that the other citizens of Venice don't share.
Two themes of the play are appearances ("All that glitters is not gold") and mercy ("The quality of mercy is not strained")--perhaps a third third theme is the appearance of mercy since Antonio's mercy toward Bassanio is modified by his lack of mercy toward Shylock. Based on the analysis of Antonio's character and on the these mentioned, I'd suggest the Appearance of Mercy as an alternate title to The Merchant of Venice.