Begin in Vancouver and ride south to Anacortes. From Anacortes, you can catch a ferry to Lopez Island, and from there you can ferry hop to Orcas and San Juan islands. Then you can go back to Anacortes and continue south. You will be riding onto Whidbey Island from there. Our WA Parks section 1 map shows this routing: http://adventurecycling.org/routes/washingtonparks.cfm?pg=detail&s=1
The San Juans are very scenic through hilly. If this is the only time you'll be in the area I'd cycle them. Bicyclists pay the passenger fare so it's much cheaper than automobiles. See the WA State ferries pages for more info: http://www.wsdot.wa.gov/ferries/info_desk/route-maps/
If you don't want to return to Anacortes you can go to Sidney on Vancouver Island and ride south to Victoria (a very interesting city with lots to do). Then you can take another ferry to Port Angeles which is located on the Olympic Peninsula. The alternative to avoid Shelton would be to ride west and south along the Olympic Peninsula from Port Angeles. At Elma you can rejoin the Pacific Coast Route. That section 1 map I mentioned above will show you how to do that.
This might help you make up your mind also: http://www.visitsanjuans.com/what-to-do/san-juan-islands-bicycling