The Provincial Museum is worth a trip. There are amazing totems and other northwest Indian artifacts. The museum has a section that uses multi-sensory experiences. When you go through the recreation of the historical port, you hear the waves and the cry of gulls, you smell the salt air, etc.
While Butchart Gardens are wonderful, I am not sure that fall is the right time of year to go there. You might check first to see what is blooming.
Make sure and taste the local treat, a Nanaimo bar, decadent and rich but worth it as a once in a while thing.
There is good shopping with art and artifacts and goods from the European Union.
Tea at the Empress Hotel is a wonderful experience if you like that sort of thing.
Note what they say: “Reservations are required and should be made direct with the hotel, one to two weeks in advance to avoid disappointment. Tables are held for ten minutes after reservation time. Please contact Resort Reservations at (250) 389–2727 or book on-line with a room reservation.”
If you like things a little more rugged, you might head over to the West coast. If you do stop at Cathedral grove. You probably don’t have enough time to get all the way to Tofino and Pacific Rim National Park, which are exquisite.
Perhaps a ferry ride to Salt Spring Island, an exquisite rural jewel and artists’ colony. Gorgeous scenery and the Canadian ferry system is so much better than the U.S. one.
Have a wonderful time.