I was thinking of comparing the compassion and camaraderie shown by the working class in Germinal and comparing it to the selfishness of the working class in L'Assommoir. Or perhaps something around the issue of alcoholism.
I think that both ideas sound like good ones. Given that Zola was a Naturalist, you could focus the dissertation on how he followed the characteristics of Naturalism in each of the novels.
Both novels contain elements of the everyday working class, both involve addictions typical to the working class of this period (alcoholism), the settings are common- as well as the characters themselves, and the fall of the characters is based upon the ever present ideology that nature is stronger than man.
I think that for a dissertation, keeping such a focused theme would harm the strength of the paper (especially since you are only focusing on two novels). If you look at the characteristics of Naturalism within the paper, you will have a lot more information as to prove your thesis more solidly.
If you do plan on looking into one of these ideas, a broader focus would be the personification of elements in both novels. The mine in Germinal is repeatedly described as a beast swallowing the men.
Once you decide, you can check out the Naturalism page on eNotes. It offers a great tool to understanding the elements of Naturalism.