There are many, many issues that contribute to the decline of fish in the Puget Sound (and elsewhere) and some of the most obvious ones have been mentioned above - habitat degradation an loss, local commercial fishing (tribal and non-tribal), increased efficiency of both the recreational and commercial fleet (sonar, GPS mapping etc). A couple of less obvious factors are:
1) I don't think many realize the scale of the impact of the commercial ocean fisheries on our returning salmon. A large percentage of fish bound for our local waters are caught in Alaska and BC.
For example, approximately 50% of all salmon caught in the SE Alaska commercial fishery are Columbia river bound fish. Ask any recreational fisherman who fishes on the west side of Vancouver Island and they will tell you about 90% of the fish they catch are Columbia River bound fish. E.g. without Columbia River hatcheries, much of the West coast of BC and Southern Alaska, wouldn't have much to fish on.
While the article I linked above talks about the percentage of the SE Alaska commercial catch that is Columbia River fish, it doesn't speak to the fraction of Columbia River bound fish that are caught prior to reaching the Columbia River. In many coastal river systems (Columbia, Grays Harbor), the estimates are that greater than 80% of the returning fish are caught prior to passing the south tip of Vancouver Island. There's no reason to think that anything different is happening to Puget Sound bound fish. So while we can complain about gill nets and purse seiners in our local waters, all of us are fishing on a small fraction of the available fish as most of them are removed by commercial operations prior to entering our local waters.
2) Another major issue is hatchery produced salmon and more specifically, the lack of cooperation between various governments on the percentage of planted fish and species planted.
Over 5 billion (yes BILLION) hatchery raised salmon are release each year by a combination of Japan, Russia, the U.S. and Canada. Of those, the vast majority that are released are pink salmon and chum salmon. All of those fish feed in roughly the same waters (the Bering sea and the N. Pacific) on roughly the same food sources (or food sources that feed other food sources such as zooplankton and krill). So those hatchery fish and wild fish are all competing with each other for the same (limited) supply of food. There are no agreements in place to limit the number of hatchery fish produced by various governments so that those produced by others have a fair chance of survival. Rather it's a "cowboy" system whereby the most aggressive regions get back the most fish. One factor in finding smaller fish each year is undoubtedly the limited food supply being split amongst increasing numbers of hatchery (and decreasing numbers of wild) fish.
Ultimately, there are many "solutions" to the problems since there are many problems. Politically, that makes it easy for each group to point at the others and assure that nothing gets done. However, one thing that is absolutely clear is that commercial salmon fishing in the ocean is largest contributor to salmon stock declines. Also commercial interests in hatchery produced fish results in a system that is not cooperative between different governmental jurisdictions.
In the U.S. we have had prohibitions on commercial harvest of land mammals since the late 1800's to early 1900's. The reason for this was clear. Everyone could see the decline of various animals (bison being a prime example) and ultimately it was agreed that commercial harvest of a public resource could not be allowed if the public was to have full benefit of the resource. Commercial harvesting of land mammals was banned much earlier in most of Europe. Ultimately, I think that the same will have to happen with commercial harvest of fish from the seas. There are too many people on the planet to feed with this finite resource and commercial exploitation of fish almost always results in a crash of the population (or sometimes an extinction).