Mission 1 - I agree, good idea
Gratitude - the alarms/barking implemented are fairly simplistic, so unfortunately they never shut off, but I can see it would be a good idea, and night time? Maybe, I was probably tired of using NVG's in so many missions
Turbulence - this was a very difficult mission to implement, the enemy is actually "disabled" from the start and re-enabled after the first objective. I did this because FDF tanks, soldiers, and Marines would decide on their own to go and kill most of the enemy, leaving the player little to do. The Takistani are literally inside the buildings from the start, then I shut off simulation and made them invisible so that friendly AI would ignore them. This seems fairly realistic to me, because they are simply hiding out until it's time to strike back at the invaders. I hope that clarifies my intentions on that.
Last mission - There is no helicopter rescue because of the expected EMP from the nuke, so HQ orders all flights to ground. I could have Ian radio HQ and have this explained, though. At any rate the original plan was to have 2 different cutscenes as you mentioned, LOL! I axed that ultimately because I want continuity with the next campaign Dark Tides, and also wanted to portray the selfless sacrifice of elite warriors. Always caught between give and take on plot decisions

I might change my mind on this later, who knows. Thanks for you ideas, it helps a lot to see how others view it, especially when it's all in my head, and I'm not sure if I conveyed enough or not.
One other thing on the last mission, Denmark is at the final firefight, but he tries to escape by vehicle. He can be stopped if your approach is right and you have enough firepower. Just letting you know.