I am assuming that by 'Faustian theme' you mean the bargain both men make with the devil to fulfill their desires. You could altogether leave the supernatural out of a paper on these two works and focus on comparing and contrasting what it is that Faustus and Dorian want. Faustus wants more than human knowledge: he wants knowledge of magic and the power it can bring. Dorian, in contrast, wants to be able to indulge in pleasure and vice while at the same time staying as beautiful as he is in his portrait and never aging. These seem to me to be very different desires, but they spring from similar roots: each character wants to make the most of traits in themselves they are most vain about or proud of. This could lead to the question of how overrating one part of ourselves can lead us into trouble.
A paper on desire could also look at how getting what they wish for leaves these two characters ultimately unfulfilled. Faustus learns magic but can't do much with it beyond making himself invisible and disrupting the pope's banquet. There is also much he can't do in the devil's bondage, such as marry, as that is a Christian sacrament. Likewise, Dorian is increasingly unhappy and dissatisfied despite staying young and lovely while his picture ages and becomes corrupt.
Both works might lead us back to the old adage to beware of getting what you wish for. One doesn't need to sell one's soul to get what one wishes for, but the results can still be bad.
Going further afield, you could look at how point of view is alike and different in the two works, or at images that are alike or different. For example, you could look at how beauty is described in both works.