> no one seems to have ever seriously asked "why do these people want to kill us".

Plenty of people have asked that question. That the answer isn't what you expect doesn't mean the question wasn't asked.

It turns out that the goal is to establish (or rather, re-establish) the Caliphate, or at least some twisted takfiri version of it.

In order to establish the Caliphate you need somewhere to put it -- namely, the Muslim countries of the Middle East.

But the countries already have states running the show. In AQ's viewpoint, they are "the near enemy". The near enemies have supporters too, including the U.S. (which was "the far enemy"). Other enemies include the United Nations (both since the UN Charter is incompatible with takfiri Sharia extremism, but also because the UN recognizes Israel), Shi'a Muslims, etc.

In one of the key decision points for OBL post-Gulf War, he decided to focus on the far enemy first instead of the near enemies.

At this point, the "crime" of the U.S. wasn't drones or bombing brown babies or anything so snide. The U.S.'s only crime was putting infidel soldiers on Arab soil to evict Iraq from Kuwait, and for maintaining regional stability for what I'm sure were completely self-serving reasons that provided no benefit whatsoever to the rest of the world.

Accordingly AQ attacked the U.S.: The 1993 World Trade Center bombings... the 1995 "Bojinka" airline bombing plots (yes, plural) that was only discovered by accident at the last second by an alert Philippine policewoman... the 1998 embassy bombings... the 2000 attack on USS Cole in Aden, Yemen.

The U.S. response was remarkably restrained throughout this entire period. Despite hundreds of Kenyans alone being killed by AQ in the 1998 bombings, the U.S. response was limited to dropping cruise missiles on known AQ training camps in Afghanistan and a chemical production facility in Sudan that showed evidence of working with AQ to produce nerve gas. The evidence was not ironclad, mind, but that was it: No boots on the ground, no roving drone patrols, no NSA massive surveillance efforts.

The problem for AQ wasn't what the U.S. was doing to the rest of the world by 2000, the problem was that the U.S. wasn't doing enough. AQ had somehow failed to get America's serious attention, and had failed to evict America completely from the Middle East, so they decided that they had to go bigger. And they did.

So while the facile "they hate us for our freedom" line is not the answer, it's not far off: They attack because Muslims still live in either approximately free societies, or tyrannies under the wrong dictator (i.e. apostate regimes). There will be no end unless they establish the Caliphate, and even that doesn't necessarily represent the end, since the stated goal of this new caliphate by Ayman al-Zawahiri is to extend jihad against the U.S. and the West.

If you want to research yourself the motives of the various and many insurgent/terrorist groups out there then there's certainly no lack of material, from the very many people who have asked the same question you say has never been asked. I'd recommend going through some of it. Articles asking (and trying to answer) this question have been published since long before 9/11. Huntington's "Clash of Civilizations" article dates to Bosnia.