Obviously what comes across as a Mary Sue can vary hugely from person to person. I absolutely adore Mr. Nutt, Glenda, and all the others. Even Trevor Likely, who I started out thinking I would hate, became very likable by the end.
One of the things I love about Terry Pratchett is his ability to write unconventional romances, and he brings that out in full force in Unseen Academicals for his unique twist on the Romeo and Juliet story and even more for the relationship between Glenda and Nutt.
Terry Pratchett's brilliant writing is there, and I appreciate the references to previous books, such as the reappearances of Rincewind and Mightily Oats, but for me what makes this book are the characters, who I find unique, sympathetic, and very human.
Perhaps it's not everyone's cup of tea, but Unseen Academicals is right up there with The Truth, Going Postal, Night Watch, and Monstrous Regiment for my favorite of Terry Pratchett's books.