As the oceans absorb CO2, the acidity increases. Not so great for our preferred fish species.

The acidity of the surface layer increases right now. And that's a big problem.

The mixing I was talking about will take a few thousand years, and I am not sure there's enough air to make a dent in the whole ocean's depths' pH level.

Probably true, but the fact that we eat all those fish is a far bigger short term problem.

I heard somewhere (rumor alert) that jellyfish and other species we don't like to eat are taking over much of the oceans, since we ate most of the fish.

Open a small business harvesting jellyfish. It is already a growth market in Asia and will be a growth market for the next 50 years in many parts of the USA:

"Southern Fishermen Cash In On Asia's Taste For Jellyfish":

http://www.npr.org/sections/thesalt/2014/01/28/267836803/sou...

"Jelly Balls Harvested by Boone Seafood Darien Georgia":

https://www.youtube.com/watch?v=laArO6Yk-W0

It's not just because of fishery collapse. The changing temperature and pH matters, too. Reefs bleaching and all that.

I wouldn't say it's a rumor. Just a possibility as reported by some researchers. Not a consensus, as far as I know, though there was a book about it summarizing the research.