There have been many posts about tis subject but let me try and sum it up.
1. Seattle- Ships that go from this port tend to use the 'Outside' route to Juneau [first port of call] This means that on the outward and inward voyages- you sail on the outside of Vancouver Island. Not much to see this way until you get to Alaskan Waters .
2. Vancouver.- All ships go the Inside Passage route between Vancouver Island and
the mainland and this is a much more interesting route [in my opinion] I have sailed both ways and would choose Vancouver every time.
You mentioned the airline into Vancouver is more expensive tan into Seattle.
However, the options of getting to Vancouver from Seattle are many including a shuttle from Seattle Airport to Vancouver, rental car [one way] railway. etc.
I always use the rental car and stay outside of Vancouver [its cheaper unless you use priceline]
All in all you have many choices but air into Vancouver should not be one of them in my opinion.. Its too expensive etc.
Let us know what you decide and have a safe and happy cruise.
I have traveled that route before and there really isn't that much difference between going to Seattle and then taking a shuttle to Vancouver or going directly to Vancouver via air, if you know the right place to purchase your airfare. For instance, America West (americawest.com) cost $299 to Vancouver and $267 to Seattle for a difference of $32 which the shuttle would cost, at the very least not to mention the added inconvenience. As far as the airfare to Vancouver from Chicago and the return from Anchorage to Chicago, it's only $399 on America West and even less if you're over 61 years old. You just have to know the in's and out's of the airline game.
There is a couple of exceptions tho..one being the Norwegian Star. This ship leaves round trip from Seattle, stays within The Inside Passage and even goes to Glacier Bay.
Getting to Vancouver from Seattle is an inconvenience both price and timewise.