Why did Pip marry Estella when Biddy was much better than her?

In Ch.39 Magwitch returns to England and shocks Pip by claiming that he is his benefactor and asserts, "Look'ee here, Pip. I'm your second father. You're my son more to me nor any son."

In Ch.50 Pip makes the startling discovery that Magwitch is Estella's father: "and the man we have in hiding down the river, is Estella's father."

This would make Pip and Estella almost brother and sister, and for Pip to marry Estella would be incestuous - something which the contemporary Victorian readers would have found impossible to accept. And that is why in all the standard editions of the novel Pip and Estella do not marry at the end of the novel and both of them part as friends:

"We are friends," said I, rising and bending over her, as she rose from the bench.

"And will continue friends apart," said Estella.

It should also be remembered that Dickens' friend, the novelist Edward Bulwer Lytton pleaded with him to unite Pip and Estella, and after much persuasion on his part Dickens did so. This version of the ending in which Pip and Estella are united in marriage was used only once by one maverick editor, namely, George Bernard Shaw in his 1937 edition of the novel.

However,most importantly in Ch.17 we find Pip struggling with his feelings concerning both Biddy and Estella. Pip confesses to Biddy that he wants to become a gentleman and when Biddy asks him, "do you want to be a gentleman, to spite her or to gain her over?" Pip is confused and replies "I don't know." This is because he has become foolishly infatuated with Estella and is unable to free himself from her power even though she is always rude to him and torments him both physically and emotionally. Pip himself admits that, "Biddy was immeasurably better than Estella" but is unable to decide to marry her or not because of his infatuation for Estella, and Pip confesses and acknowledges this fact: "All the while knowing the madness of my heart to be so very mad and misplaced." Finally, he pleads with Biddy in the follwing manner:

"Biddy ... I wish you could put me right ... If I could only get myself to fall in love with you ... that would be the thing for me." To which Biddy replies very sagely, "But you never will, you see."