I agree with some of your points regarding the bosses & use of the vehicle. The
'stealth' Batmobile elements were pretty silly overall I thought considering the sheer size of the thing & to your point about wasted boss fights, the biggest one I can remember being irritated with was the Deathstroke one & it was purely on the basis that I loved the Deathstroke boss fight in Arkham Origins because he was adaptive of the attacks you were using on him. The Shivia one was also good from Origins from memory.. both involved achievements that I spent a while trying to get.
The Firefly one I didn't mind because if I recall wasn't it basically you chasing him around the city on his jetpack? Until you get close enough to taze him or shoot him down. That one was fine IMO.
The Riddler tracks & trophies I personally loved on my 2nd playthrough I went for them all, I get those are personal preference though because I know a lot of people didn't like the Arkham City Riddler stuff because some of them required intricate gliding.
You do come across the Arkham Knight a couple of times, I think he's the one in the drill tank if I'm not mistaken but his
'boss' fight isn't in the Batmobile. It's a stealth room & he's on one of the gargoyles with a sniper & a bunch of sensors/traps/henchmen everywhere if I recall.
I get your overall point(s) though that you were burnt out with the vehicles reliance & use in the story.