Ok, I have a lot to unpack on this one, since I've played it from beginning to end (except the DLC missions), but first: Merry Christimas.
First off, the flamethrower boss. You need to shoot him enough times on one of his fuel tanks so they will explode, it will not kill him but will deal a lot of damage and destroy his armor. I could say you messed up, but I also have to agree that this is poorly explained by the game itself. (although it shows a yellow marker when you hit it)
As for story, well... First, some details are better explained in logs you find spread out in the city in typical Ubisoft open-world fashion, but it's still poorly explained in typical Ubisoft open-world fashion, so I don't blame you for trying to understand the game's story just by playing the main missions.
But of course, the premise is executed in a very bland way. There's socio-political themes floating around, but nothing is explored properly, and all characters are forgettable. But there's a good reason for that, you gave it the award "Secret Genius?" and I could say there's one, but it's not what you think.
The "secret genius" is that the themes and overall idea of the premise are not there because it has a meaningful message to say, they are there to fool you into thinking there's a meaningful message. In other words, they are there to make the plot sound "deep". Believe me, I can tell from experience that this hack writing tactic can work sometimes, especially if you are younger and/or don't have much clue about this stuff, just like bikini armor does to the mind of a horny teenager.
Still pressing "X" to doubt? Why don't take a look back at The Crew? Sure, it was a complete different beast compared to The Division, but it was trying to be a more "mature" drama story in a video game. Because, according to some people at least, video game plots usually suck. And that's a trend that I'm noticing a LOT with AAA games over the decades: They are trying way to hard to make the games feel more "cinematic", and not just with brown filters, but also with writing.
Don't get me wrong, I do think video games CAN have good writing if given the chance, but that will not happen if we still are trying to write them like movies. Which makes me think it could be a good idea for you to cover a David Cage game. Because for a guy that ranted a lot about the industry needing to "mature", his plots are juvenile. (especially Indigo Prophecy)