We just visited the island and Victoria (the BC capital city on the island) in early September. I had been to Vancouver city and area the same time 4 years earlier and liked it (great time of year to visit), but I LOVED Victoria and the parts of the island we had time to see this trip. Cottages and very nice apartment rentals are the way to go there. It's amazing what you can find for around $100 a night -- a few places even come with kayaks!
We had hoped to make it up to Campbell River and had looked into a lovely cabin on Puget Sound there, planning to do day trips into Strathcona Provincial Park. Here's the link.
Victoria is the most civilized and pleasant city I've ever visited in North America. Natural History Museum is terrific and it's a nice city to walk around with unique shops and a variety of great restaurants. Beacon Hill park at the southeast end of downtown has floral gardens, ponds, fountains, wildlife, a petting zoo and trails that go all the way to the Sound. We didn't make it to Butchart Gardens but heard they are wonderful. You can rent bikes and ride the Galloping Goose Trail west along the Strait of Juan de Fuca. While in the city we stayed at the Arbutus Inn 2 miles north on Douglas Street -- very handy, clean and reasonably priced.
You can take the car ferry across Puget Sound through the San Juan Islands (highly recommended) to Anacortes and drive up to Vancouver city. I found Vancouver to be too crowded and hectic for my tastes, but a drive northeast to Deep Cove harbor on Indian Arm inlet is a great place for a kayaking day trip with top notch sea kayaks and gear to rent right at the marina. Or drive up Howe Sound to the west and then north towards Whistler, site of the 2010 winter olympics.
But, honestly, I could spend a month on Vancouver Island and never be bored.