I just finished a play through where I sided with the Institute and had to destroy the BoS and their flying ship. It was a blast battling all the BoS Knights, Paladins and scribes. I was disappointed you can't wipe out Maxson, he just drops to his knees and becomes invulnerable. Then you get teleported out.

My main gripe with the scenario is that while I was fighting the BoS the weather was clear and sunny. After I got teleported to the other side of the river it suddenly became heavily foggy and I couldn't see a thing. I heard all these explosions but saw nothing.

A suggestion: Make sure the weather is forced to any type of weather other than foggy, especially when it magically switches to foggy when literally seconds before it was clear and sunny.

Are you sure that Maxson wasn't just near death? I played with Institute and killed him in the battle, then took his battle coat and weapon just before I got teleported away.

Yeah, I can imagine the disappointment due to the weather...

Yeah, I took out Maxson.

AD VICTORIUM IN HELL!

SS atop Liberty Prime: "Okay, this battle is going fine. Soon, the Synth will-"

*strong laser beams strike the SS from behind*

SS: "What the hell? How did anyone get behind me?!"

*sees a BoS power armor on the roof*

SS: "How did you climb there? And just who... Maxson? I see..."

*SS jumps onto the roof and reloads Deliverer*

SS: "So you want to have this up and personal, huh? Just you and me..."

But seriously, does he jump out of a Vertibird?

Yeah, he was up near the top of the gantry on that ledge. I was shooting him a lot, he dropped to one knee and I kept shooting but he was taking no damage and then about 3 seconds later I got teleported out. I was using the Overseer's Guadian on him. I thought that either they were keeping him in an unknown state to maybe use him later in some DLC or I was hitting a piece of armour that was blocking all damage.

This is clearly another bug then. if you are on PC, you can use the console to remove his essential status.

I totally screwed up the way the final mission was played.

I didn't realize we were supposed to sneak into the BoS Airport so I attempted to fight the entirety of the BoS before entering.

Lots and lots of stimpacks, hiding, stealth, and Piper falling back with me behind cover.

When I finally got to the Grand Finale section, the Synths were like, "Huh, not much resistance."

Well, knight, that's why you never fit in the Brotherhood! You should listen to mission briefings with more attention!

Must have been horrifying for the BoS to find out that one man was all it took to destroy them XP