I personally think Harry Potter overall is a better book than Twilight (not putting down Twilight in any way, love that series also) BUT ! Harry Potter I feel is way more intriguing, J.K. Rowling kept you guessing right to the end. Whereas in Twilight, sure, Edward left Bella which confused everyone but I think it was all to obvious that he would come back and they would end up together, which is exactly what happened. In every Harry Potter book the new monsters Harry would face and the new twists and turns Voldemort throws at him also keeps you going. Also, I think that twilight is geared mainly towards teenage girls, I personally haven't heard of any male loving the book, and with Harry Potter everyone can read the book and fall in love!
Overall I do think this is fully opinionated and there is no win in this situation