I've seen some Q2A sites do have homemade notification settings. So I don't think building a notification system is extremely hard.
With my bullshit knowledge, I think we can create a table to store user settings like question_notify, answer_notify, comment_notify...
The notify column in qa_posts becomes unnecessary.
Whether to send mails or not can be done with event module by first checking at the notify table.
Finally, some housekeeping jobs like to create a button in the user profiles.
I believe someone like esqeudero can do it in 1 and 1/2 days.