Increased CO2 over extended time periods would lead to fewer large fish due to the process of ocean acidification (my understanding is that smaller fish cope better than larger fish in acid environments, that's not to say they will be prolific in an acidic ocean, however). Phytoplankton would do very well though, assuming it can adapt to the acidification and warming.

Most Earth-based counters historically have involved megaflora sequestering CO2 as they die, however this is over the scale of hundreds of thousands of years, and requires large expanses of land to host plants to do the sequestering. We've doled out most of this land already, so this isn't likely to happen. If you're looking for a deus ex machina, you might wanna hold out for a supervolcano to eject a bunch of material into the atmosphere.