Hi Alaska Novice,
Can help with a few questions..... In Junerau, try to plan a whale watching excursion, we went through Capt. Larry: http://www.alaskawhalewatching.com/
We had a great time on this tour, saw lots of whales.
You may get some ideas of what to do in Vancouver at this site: http://www.virtualvancouver.com/
As for the airline traveling, since you will be using an "open jaw" flight, you may want to check with the travel agent, sometimes with these kinds of flights they can get a better price, plus you will be doing a deviation for the extra days, which is a great idea. Vancouver is a lovely town, be sure to walk through Gastown, nice shops.
As for the upgraded cabin, I would definitely say yes
get the balcony, especially in Alaska, you don't want to miss anything, its absolutely breathtaking. We recently did our first Alaska cruise and a balcony is almost a must if you can swing it, you will be suprised how much time you do spend there.
As for the weather while you are up there, expect anything and some rain, we were lucky, only had one afternoon of rain in Juneau for the entire week, but basically, you should love the cruise, have fun!