In Just Cause they don't have to worry about player killing innocent civilians. You are not going to get a game over screen if the player fails to stop a crane or other debris from falling onto a group of civilians in Just Cause. That's why a sequence like that does not require QETs in Just Cause. If that kind of freedom is given in Spiderman game then you will have people who just choose to go after the helicopter without bothering to stop the crane. If the game gives game over screen for failing to stop the crane, then people will complain that game made it seem as though there was a choice when there was none. If they want to create a set piece that keeps up the pace of the sequence while also not frustrating player, then QETs are acceptable compromise. If they get rid of the set piece altogether then people will say that there no big "Spiderman" moment where he saves the day and gets the bad guy in the nick of time. Although I agree that button prompts should be normal web buttons (trigger and shoulder buttons) rather than X.
tbh I would just prefer the mission failure thing. Also, I hope they aren't being too uptight about the game. I feel that games are much more fun when the developers aren't afraid of having the player "break" the game. I should have the option to be an asshole Spider-man if I want. I want to string people up in a chain and hang them from the highest rooftop. Stuff like that would be insanely fun.
I suppose it all just comes down to what you want out of this game. I want a physics sandbox thing that gives you the freedom to goof around and get funny scenarios. What they've shown so far, however, is more along the lines of carefully constructed, scripted cinematic experience.