Project Exonaut takes place after Fusion Fall.After the battle against ended, the denizens of the Cartoon Network universe decided to found the Exonaut Academy to ensure that Earth's safety would never be threatened again. The Humongous Mecha were designed after the heroes who perished in the war, in their honour. As a side note, this troper seems to be the only one who finds the concept of Project Exonaut fucking awesome. Ben 10 and Generator Rex with the zany world of Adventure Time, for example. The player characters are also toons which explains why there's no problem sending kids to fight aliens.
Why the Powerpuff Girls have realistic designs.It's been about five years since the events in the series, I'm guessing. Enough time for them to grow their fingers. Why? Simple, they were essentially created as-is clothes and all in their show. They're crime fighting fetuses. So when they got older, their proportions changed, the skin between their fingers died and their eyes became, relatively, more reasonable.
Jack undid the future that is Aku.Jack indicates in the game that Aku is a bigger threat than Fuse will ever be, and yet, here's Jacky. Why didn't he return to the past? He can't. Seriously, only Aku had the power to send him back. After defeating Aku, the universe changed around him, like how in Ego Trip, the future changed immediately after Dee Dee switched the flow of the Neurotomic Protocore from negative to positive. Thus Jack was stuck in the altered present.
Dexter decided not to become a wuss.This may not even count as a wild mass guess, but seeing as how he's got his own company, Dexter apparently decided to fore-go all that working for the man crap and just run his life the way he wanted to.
Dexter and Blossom are, or will end up, together.Cartoon Network was originally going to hire Bleedman (writer of Powerpuff Girls Doujinshi) to work on this, but he turned them down. What is it everyone finds so interesting around that series again? Plus, picking Dex as your guide is the only way to get missions from Blossom.
FusionFall is a loose adaption of 2007's "Cartoon Network Invaded" eventA Crisis Crossover about aliens invading the Cartoon Network universe? Seems plausible to this trooper.