Yes, it can rightly be said that the play The Merchant of Venice has divergent plots dealing with multiple issues. But stating that, I guess most of the plays and novels do have the same aspects due to the very nature of those genres.
 
The Bond story has been the most prominent plot in the play. Bassanio needs some money as he wishes to go to Belmont to woo Portia. But Antonio has no ready money with which he can help his friend. So, they make a bond with Shylock and borrow the money in Antonio’s name. Later the news comes that Antonio has lost all his wealth as his ships have been destroyed in the storm. So he cannot return Shylock’s money on time and faces the danger of losing his life. Finally he is saved by Portia’s clever argument in the court.
 
The Casket Story is another important story-line in the play. Portia’s father makes a will before his death and makes an arrangement of three caskets one of which contains her picture. Whoever chooses the right casket wins Portia. Prince of Morocco and many others fail while Bassanio is the only one who makes it count. He marries Portia in the end.
 
The casket story and the bond story are interlinked with Bassanio present everywhere and the casket story requiring the bond story happen at all. But there are others sub-plots in the play. We see the relationships like Shylock and Jessica, Launcelot and Gobbo, Bassanio and Antonio, Portia and Nerrisa, Bassanio and Gratiano, Nerrisa and Gratiano, Jessica and Lorenzo and so on. 
 
All these plots and sub-plots convey distinctive social issues and human characteristics like friendship, melancholy, love, gratitude, racial and religious hatred, women’s position in the society, humour and irony and even pure fun and enjoyment. Though the main interest of the play has been the discrimination between the Christians and the Jews, Shakespeare has tried to present a complete picture of the society through these various plots of the play The Merchant of Venice.