The larger ships, even the ones that depart out of Vancouver, do not sail through the lower portion of the inside passage (the Seymour Narrows) which is an incredible experience.
AND
Many smaller ships, even though they depart out of Vancouver, do so in the evening so much of the most beautiful sailing is done in the dark!
If you really want to enjoy the lower inside passage, you need to target a sailing itinerary that is compatible. I love sailing Alaska, and I enjoy the port stops, but seems like most of the big lines and bigger ships have optimized their itineraries to maximize port times, thus shortening the enjoyment of sailing through the narrow and beautiful places. :(