Maybe which way you go should be related to when you go. Not last year for sure, but often the weather up north can be relatively undesirable in early summer. True in BC as well, but generally a good bit less so, it seems to me. I'd probably start from WA and head north, rather than the other way around. Get off the water in Skagway by roughly the end of August, and the last part of your trip, way up north, could be timed pretty well. I like the weather odds in SE AK, especially the northern part of it, after roughly the end of June.
Unless you're sailing, I don't think prevailing winds have much to do with your choice. Often the roughest weather comes from the SE, but prevailing winds (in settled weather) are from the NW. You can avoid much of this NW wind by doing much of your traveling earlier in the day, rather than mid afternoon, when the NW wind is usually the strongest. Prevailing NW may be 15-20 knots, but a front coming through often creates SE winds of 20-35 or more, especially in certain places.
Where you are, and as a consequence how much fetch the wind has in which to build up waves, is a key factor. That's why the big open crossings and long straight channels tend to be a challenge.
You could learn a good bit more of what to expect from the Douglass cruising guides, one for SE AK and two more for BC:
www.fineedge.com
You might as well get them sooner, because you're going to need them anyway when you go.
For more recreational reading that's also educational, look up the books of Joe Upon, particularly Alaska Blues, and Journeys through the Inside Passage.
Also there's "How to Cruise to Alaska Without Rocking the Boat Too Much" by Walt Woodward - old, but some pretty good information.
and of course my book....