Yey! You finished the campaign! And I enjoyed watching it. It's too bad I cannot join the live stream because of the time difference. When you went live, it was May 30 at 2am in my place. I could have added some hints. And I could have explained a little the post credit scene. But I will do so in this post with no spoilers. Please do note that this is AFR universe. And so...
The Blue Guardian is the patriarch leader of the Shivan race, an enigmatic race that occupies 3/4 of the galaxy. What the GTVA fought in FS1 and FS2 is just a rouge faction led by Grond (the planet Shiva was just an outpost which the GTVA mistakenly called the Shivan home planet). Again, I stress that this is AFR universe. Now, Grond's actions angered the Ancient (the purple ship in the post credits scene) and the Blue Guardian was trying rectify the chaos caused by Grond and he chose to influence John Richter as a tool to solve the problem, the human he refered to as the "receptor." The Ancient, however, believes that Richter will be a problem in the future. This is what the post credits scene dialogue was all about.
And this mystery will be answered in the sequel, The Blue Guardian. The title itself hints the return of this blue shivan.
One tiny spoiler: John Richter is an admiral six months later (the time between AFR and AF2). He is CO of the 23rd Battlegroup. As the hero of the GTVA, he skipped the Commodore rank. But he is no longer the main protagonist. AF2's protagonist is a female.
By the way, you do get promoted very fast in times of war which I greatly exaggerated in AFR, sacrificing some realism.
AFR is a "player-driven" campaign. No character plot. Just a war campaign. Very little dialogue. If there is a story, it's the mission themselves. A simple story of how the GTVA win it this time. Like you said, an experience which I actually intended. However, there are also clues of some undercurrent going on which pave the way for the sequel.
AF2:TBG is a "character-driven" campaign. That means it has a real story now. A real character and story progression with a protagonist and a bad ass villain. More dialogues. And it's a bit serious. But this time, I only wrote less than half of the campaign or maybe 20%. My main writer is CT27. This is his work, I just designed the missions and directed the whole chaos.
EDIT: ...And yes, there is chaos. A tradition of "The Aftermath" universe. You go pew pew! But the enemies will really go pew pew on you too and drive you really nuts!