Although unfinished, The Mystery of Edwin Drood would have been a masterpiece. Although we do not know the ending, there is enough of the book that we have to describe some themes. In the books you mentioned, Dickens developed some of the same themes, perfecting them as he continued writing throughout his career. It is not a coincidence that Great Expectations and Edwin Drood take place partially in the same town, the place where Dickens grew up.
The first theme present in all three is duality. In A Tale of Two Cities, Dickens explored the idea first in a more simplistic way with two characters who look alike but are very different, though they are in love with the same girl. Though they are two people, Carton and Darnay play two sides of the same character. The lost alcoholic and the noble expatriate are both heroes in their own way. In Great Expectations, we have two sides of several characters, most notably Wemmick and Pip, with the latter growing and changing. Finally, in Edwin Drood Jasper also has two sides, spurred on by a secret life and drug addiction.
Guilt is the second major theme in these works. Drood follows the other two as Dickens’s final exploration of guilt and the human psyche. All three have elements of mystery, more and more as we move closer to the end of Dickens’s career. Great Expectations is about the effects of guilt on a person as well, but in the less sophisticated Pip. In A Tale of Two Cities, Carton, Daray, Dr. Manette and even Madame Defarge are consumed by guilt, although hers turns to revenge.