The Red Skull has a seemingly infinite list of Kick the Dog and Shoot the Shaggy Dog moments, becoming perhaps the biggest Hate Sink in the entire Ultimate Marvel line. However, when it is revealed his life's mission has been to travel back in time to rescue his father and grow up with a real family, his reasoning for it becomes clear... he WILL reach his goals by any means necessary. His actions are horrific beyond description, yes, but none of it will have actually happened if he succeeds.
Those who have read The Ultimates 2 in which Hawkeye's entire family in murdered in front of him will understand the personality change he undergoes in Ultimates 3. He's clearly suffering from post traumatic stress disorder as a result of what happened to him but it's clear that he's not receiving any help for it. You'd think he might not be welcome on the team without first undergoing a fair deal of therapy, but recall the the whole point of the Ultimate universe is to be more grounded and realistic than mainstream Marvel comics. In real life, there is something of a stigma in the military for those who seek therapy/counseling after a traumatic experience in combat. Hawkeye is a soldier and part of the reason he doesn't seek help may be be because of how others would judge him for it.
Captain America being more abrasive than his 616 counterpart is usually chalked up to him having antiquated values, having come from a time when sentimentality was considered "unmanly", but it could also come from his angst over being a Fish out of Temporal Water.
The DNA-specific bullet. Ultron calls this whole thing a crime of passion, and he apparently only shot Scarlet Witch the moment he saw that she and Pietro were lovers. Yet he'd been carrying a bullet coded to her DNA around all this time?
Captain America woke up in the XXI century, to find that all the people he once knew are now elders or dead, and the world has changed beyond recognition. Nick Fury gives him some confort: the flag of the US has not changed, it's The Constant. Unfortunately, not even the flag is like Cap remembers: as Alaska and Hawaii became states in 1959, now the flag has two more stars than in 1945.
At least the general look of the flag is still the same, even with the two extra stars.
