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 laughs—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, 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. 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.