Love Quebec City! Been there many times during the summer and the winter but never in the fall. I suspect that the city will be relatively quiet (ie no big festivals happening). However, you will still have a great time exploring all the shops, restaurants, pubs, clubs and sight seeing stuff. The people of Quebec are friendly and will proudly tell you about all the great things their city has to offer.
Definitely get a place in the historic district (vieux Quebec) so that you will within a short walk to all the coolest things in the city.
If you get the urge to do something healthy you could rent a bike and take an amazing ride along the St Lawrence river. There is an incredible bike trail that follows the river and is very scenic. I'm pretty sure it is on the opposite side of the river in the town of Levis. You just hop on the ferry to get there.
And, keep in mind that fewer people speak english in Quebec City than in Montreal. French is the only language most people speak even though they may have studied english in school. It's a great place to brush up on your french