I grew up on the shores of Lake Michigan, fishing the beaches and tribs for salmon. I moved out west in the mid 90's, right about the time the invasive mussels arrived. Now when I return to visit I am amazed at how different the water looks, clearer and a totally different color blue. I miss the days of casting to schools of salmon chasing alewives along the beaches at first light, but those days are pretty much gone.
Round gobies have also taken root in the ecosystem and love eating mussels, and lake trout love eating gobies. So much that they make up to 80% of a lake trout's diet now. So while the Chinook fishery is not what it once was - it's still not so bad actually, and now we have some ridiculous lake trout fishing, and it seems out walleye populations have been booming lately.
The salmon over here(Huron-essentially same body of water) are generally smaller but super weary, because of the gin clear water. I use 15lb flouro and I have noticed an increase in bites, and if you aren't using long leads, you'll get blanked. I've also heard that these clear water fish fight harder because they need that extra speed to hunt in the clear water... I beleive it, from what I've experienced a 15lb Huron Chinook fought harder than the few 15lbers I caught in Tofino last summer... although the ocean Chinooks would have to elude larger predators, I think their average speed is probably less.
"The Death and Life of the Great Lakes", by Dan Egan is a great book that goes into greater detail of the issues mentioned by the OP.
I would recommend it to all fishers, even those that don't live in or around the Great Lakes.
The problems that came up the St. Lawrence Seaway to plague the Great Lakes have exited the Great Lakes, when they changed the direction of the Chicago River, and now threaten and plague the rest of the country.
And as mentioned in the article, Carp are finding their way in through the back door as well.