That's an aside with no direct comment on the Hydra infiltration, and regrading the Battle of New York, the WSC's launching a nuclear missile at Manhattan (and the unprecedented mass death it would have caused) should have been a solid, tonal continuity change for all MCU characters--super-powered or not, but that entire matter (remember...it was a nuclear missile fired at Manhattan) was unrealistically swept away in favor of dealing with Project Insight. Long before Civil War, the MCU should have been in the grip of a fever of anger and paranoia about these shadowy "global caretaker" organizations deciding from (their version of) "On High" to annihilate mass populations without so much as safeguard or counter, other than Fury & Iron Man's attempt to stop it.
You're assuming that the WSC's role in this was made public, things were chaotic enough most of the people in NYC wouldn't have realized what was happening or that a nuke got fired at them.. Plus Hydra itself would've been working hard to keep people from asking questions.
But, it was--apparently--more important to just jump to Civil War, with its focus on superheroes being the problem, than "complicate" the MCU by moving the story in the natural direction of the world not trusting clearly dangerous organizations.
Not complicate things, just keep focus on the MCU Heroes. Because MCU is about the heroes, not the villains.
Why not have both, and steer the MCU in a believable direction, rather than halfway with the only logical movements happening in TWS / CW? Too dark for those who want G.I. Joe / Star Wars-ian quips and just moving on to the next set up for big fights?
No, because there's not much of a story there for the heroes and internal conflict.
Comic readers expected more generations ago, and movie audiences--like those criticizing certain parts of the MCU, also expect that.
No, they expect the heroes to all wear black leather and for all fantastical elements to be stripped away.
Barely. The plot was overflowing with cartoon fights with flying robots, a pointless, emotion-free death of Quicksilver and another big spectacle to end the film..oh, and yet more Easter eggs about Infinity.
If you dislike the wondrous, maybe.
Two, many of the Marvel movies have been blasted as being hollow, illogical or inspiring yawns.
Mainly by those who hate the wondrous and go for that bankrupt "grounded" stuff.
When this era of superhero films is long gone, I will bet you that the path of the DC films with weather the storm / hold up with its consistent development better than most MCU films that might be seen as Transformers in tights, with the exception of The Winter Soldier...the film some MCU fans complained was "too dark & edgy." Go figure.
DC's got little consistent development going for it, really.