My vote is option 2 or 3. Glacier Bay and
Tracy arm's a nice option. We preferred the Vancouver round trip too. More inside passage sailing and our ship got to Juneau in the morning which I liked. Our Seattle passage got to Juneau at 2pm which wasn't as good for us. Of course I assume that was because Juneau was our first port. The stop in Victoria arrived at about 7pm or so and that was mostly a waste of time for us other than obeying the Jones act law.
Hubbard Glacier is awsome but I do think that Glacier Bay was nicer.
We preferred Skagway over Sitka too.
Oh, you can't go wrong. It's awesome up there. We're all very opinionated on our likes and dislikes so you really have to work with what you like as well. Don't get us started on the balcony vs inside cabin debate!