Grayson's reaction to Ishi's "sense of humor comin' back"; he might not actually think it's a joke. Ishi says he intended no humor, and seconds later, Hunt laugh—or pretends to laugh—at Ishi's "murder holes" remark, which wasn't that funny in the first place. He's been reaching out to Ishi the entire level, only to be rebuffed. He really does care about Ishi(no, not like that), and this is just the latest attempt.
Why would any competent military leader implement the skillpoints system? It encourages sadism, dehumanizes enemies, and makes a game out of dea—oh, wait, Sarrano. Carry on.
When Trishka gives you 15 seconds to solve the little riddle of clearing the path in Chapter 4-1, she will call you a great douchebag if you cannot solve it. At first it might not make sense, but if you solve it, her reward for you will be willing to hear what Grayson have to say, which is to forgive Ishi since he is not a bad guy. This might imply that Trishka is calling YOU, the player, a douchebag because you have all the chance to solve the puzzle even if you don't know the answer (by reloading the checkpoint after she pointed out for you), but ignored it anyway and thus wasting Grayson's chance to tell Trishka to forgive Ishi.
Wondering why kicking some one slows them down and sends them flying? Gravity boots. During the Prologue when your heading down the side of the building Doc was talking about the new gravity boots. I'm not 100% on gravity but i'm pretty positive it works via pressure and force pushing everything down(At least at it's most basic dumb downed level)But if to much gravity was place they would sink threw the ground. So the boots provide gravity to push the user down but repel things away. Kick a mook and temporarily remove the effects of gravity on them=Slow motion upward flying
"That's a lot of bags" in the airport. Which makes you wonder if the evacuation effort was actually any good.
During the workers' revolution, the shields protecting the city from gamma storms were destroyed to eliminate the toxic waste they produced. Okay, great, but now that radiation is RAINING DOWN ON THE CITY. And no one saw it coming until it was too late. You'd think at least one of them would have thought of that.
Perhaps not. The worker's complex/prison was underground, and safe from the gamma storms. Also, the gamma storms were a distant issue that could be solved later, the toxic waste problem needed to be taken care of now.