Alienation is a good theme for the novel. The monster feels alienated because of the way he was created. So is Dr. Frankenstein.
Below is a link for themes, the first of which is alienation.
As for quotations, I think you will find this link useful for quotes related to alienation:
Like Fra Claude Frollo of Victor Hugo's magnificent work, Notre-Dame de Paris (The Hunchback of Notre Dame), Victor Frankenstein delves dangerously too far into science. As a result, his personal desires supercede what is reasonable and he, like Frollo, endanger the lives of others.
The selfish pride of Victo, the theme of the hubris of science, is his nemesis:
Yet at the idea that the fiend should live and be triumphant, my rage and vengeance returned, and like a mighty tide, overwhelmed every other feeling. After a slight repose, during which the spirits of the dead hovered round and instigated me to toil and revenge, I prepared for my journey.
There are plenty of themes in this great text. For me, the most important and most prominent theme is the dangers of playing God, and the idea of how pushing against the boundaries of knowledge can actually have unforeseen ramifications that can be potentially dangerous or catastrophic. This is what Frankestein realises and Walton learns in the book.