I agree with the eNotes analysis here which identifies the main conflict and theme as the tension between order and disorder. As Dickens is exploring the ramificiations of the French Revolution, this is necessarily the central conflict.
Here is the excerpt from that analysis. You can find out more about this theme and others by visiting the link below.
Order and Disorder
The story of A Tale of Two Cities takes place during the turbulent years of the French Revolution. Dickens stresses the chaos of Revolutionary France by using images of the ocean. He calls the Paris mob a "living sea," and compares Ernest Defarge to a man caught in a whirlpool. Defarge and his wife are both at the center of revolutionary activity in Paris, just as their lives are at the center of the whirlpool. Order breaks down once again in the second chapter of the third book, "The Grindstone." "Dickens deliberately set Darnay's return to Paris and arrest at the time of the September Massacres," writes Ruth Glancy in A Tale of Two Cities: Dickens's Revolutionary Novel, "a four-day execution of 1,089 prisoners from four Paris prisons, condemned in minutes each by … 'sudden Courts of Wild Justice.'" Contrasted to the chaos of Paris is the order of England: Dr. Manette's peaceful home in Soho is a place of refuge for Darnay, Carton, and Mr. Lorry, while even Tellson's Bank serves as a center of calmness in the whirlpool of Revolutionary Paris.