Let me clarify something about our trip out of Seattle. The first night we went outside of Vancouver Island but when we woke the next morning there was land on both sides of the ship and for the rest of the trip until the last afternoon heading to Victoria. I have read on this site that this is not always the case however. We weren't all that close to the land but it was visable. The Vancouver trips we took there were times where the land was so close I think we could have thrown a baseball from the ship and hit land. Now that's what I called the Inside Passage!
If you go the Juneau, Ketchikan, Skagway, Glacier Bay itinerary you'll be inside virtually the whole trip except as noted above from Seattle.
To go to Sitka and Hubbard Glacier you will leave the inside passage (on the major cruise lines). We had some rough seas those days.
All of us that have cruised Alaska are quite opionated so take everything we say with a grain of salt. You really can't make a wrong choice. Alaska is awsome.