How are women presented in the novel?

For the most part, it would appear that the female characters in Frankenstein—which include Justine Moritz (young William's governess) and Elizabeth (Victor's love and confidant)—are little more than victims whose untimely deaths provide turning points for the plot; slated for the Monster's murderous "conquests." The protagonist of this story is a man, and to a certain extent the reader could see it as a cautionary tale against masculine hubris. The implication is that men of science, in seeking to reorder Nature's act of creation, cannot help but see their plans go violently awry.
Another female spirit that influences the trajectory of the plot is the Monster's mate, but she's an abandoned abstraction—a further betrayal by Victor toward his wraithlike progeny—and not a character.
However, Mary Shelley's own life must have been informed by the structure and synthesis of contemporary (to the 1800s) affairs. Elizabeth is a credible stand-in for Mary Shelley herself, in that she has a formidable, questing intellect and is a possible foil for Victor's dogged scientific pursuits. While I’m not pointing to a direct equivalence between Shelley and Elizabeth, Elizabeth is a dimensional being in the novel, hardly one of the scream queens that she's reduced to in Frankenstein’s numerous media adaptions.
The novel has been seen as a cornerstone work in Women's Studies. Frankenstein scholar Susan Tyler Hitchcock notes that there were a considerable number of women-of-letters during the developmental era of the novel, but—as they were flying in the face of convention—they tended to publish under pseudonyms.
Barnard College professor Ellen Moers directly links Shelley's life experience (as a pregnant sixteen-year-old) with the creation of Frankenstein and has:

proposed a new feminist definition of the Gothic as literature whose purpose is to "to scare" by reaching "down into the depths of the soul" and getting "to the body itself, . . . quickly arousing and quickly allaying the physiological reactions to fear. (Frankenstein: A Cultural History, Hitchcock.)