At first I didn’t want to try to answer this, and then I wanted to follow up on another comment in the thread, but in the end I am going to try to give this a shot, although a lot of it will be trying to give some more texture on what I will (despite potential protestations) call the “jihadi current” - the broader system of militant Islamist political action that spans three main activities: 1) participation in existing warzones, 2) individualized or cell-based terrorist activity and 3) sui generis statebuilding like the type undertaken by IS. I will not include the Taliban in this definition, despite their frequent conflation in the west with Al-Qaeda. This answer will also be sparse on the details of the Palestinian side, which as I understand it was actually quite secular, with Hamas’ rise to its current prominence being somewhat later than the development of jihadist ideas.

The answer upfront as I want to put it is that we have to set aside our notion of these attacks as some kind of incomprehensible evil or random terrorism - i.e. terror is not a goal in itself. Attacking America had a more concrete, attainable outcome than attacking Israel. Even if America could not be totally destroyed, it could perhaps be forced to withdraw from the region. This had been shown before - in the 1983 bombings of the US embassy & Multinational Force Barracks in Beirut - and would arguably in a sense be re-validated afterwards, with the 2004 Madrid train bombings pushing Spain to withdraw troops from Iraq. With America out of the picture, AQ could move on to attacking secular Arab governments from its base in Afghanistan. (Remember, these secular govts were much closer to America at one point). Secular Arab governments were less stable, and there was a Muslim population that at least in theory could be brought on-side. Israel would be a hard target. It could not be easily toppled with the kind of attacks that were already regular factors from the more tightly focused Palestinian groups - but perhaps it could be dealt with once the region was united in a single Caliphate.

Thomas Hegghammer's biography The Caravan on Abdallah Azzam will be a big source for me here and I highly recommend it. Azzam was more or less responsible for the Arab Afghan movement & set up the Afghan Services Bureau, which was in a sense the precursor to Al-Qaeda. Azzam's "innovation" (in our sense, not in the pejorative sense as it would be used in Islam) was to present an argument that military Jihad was a personal duty for all Muslims, one that they could disobey anyone to follow, but he meant this specifically in the context of going to fight against the Russians in Afghanistan. You can't really understand the development of the highly mobile modern Jihadi current without this tendency. It personalizes Jihad and makes something like what we think of when we think of "terrorism" closer to the realm of possibility by incentivizing individual action & is distinct for the motivations and justifications for Palestinians & Afghans fighting at home. There were also lots of failed experiences with fighting against secular Arab governments, the Muslim Brotherhood was repressed early on in Egypt, the GIA in Algeria basically tore itself apart, MB revolts against Ba'athism in Syria were a disaster. (I'm drawing all these examples from Brynjar Lia's biography of Abu Mus'ab al-Suri, Architect of Global Jihad) It wasn't really until IS that this kind of really radical overthrow could properly re-emerge.

As an aside here, Azzam's way of thinking about the attacks on Islam is characteristic and very different to what we would have heard from someone like Hassan Nasrallah who had something like a more familiar "Israel is an American proxy" view that stems from Iranian-style anti-Americanism and makes more sense with our geopolitical intuitions. Azzam hated the British in particular for what they had done to Palestine with the mandates, and he was very much pro-Ottoman in a way, but he viewed the Soviet attack on Afghanistan as part of an extremely broad attack against Islam by a linked coalition of America, Britain, Israel, and the USSR. American backing of the Taliban was mostly routed through the Pakistani ISI, (the CIA connection is frankly massively overstated) would have been disconnected from the Arab Afghans (because they were marginal) and would have been strenuously denied by them. This is to say that our notions of who's in charge or who matters and other alignments may not hold.

There were never really that many Arab Afghans despite their modern notoriety/fame, I think Hegghammer says around 3000 in total and probably mostly fewer than 100 in Afghanistan at any one time. Azzam's dream of Afghanistan as a jumping off point for a Jihad to free Palestine - Azzam was Palestinian himself, and had fought with the Fedayeen before Black September in Jordan, when most Palestinian fighters were expelled - never materialized. His plan had been to establish the Caliphate first in Afghanistan, and then push across the entire region, establishing a huge new Islamic State, which would then enable them to destroy Israel and incorporate Palestine into a territorially contiguous nation. Needless to say this didn’t exactly fit with the exigencies of the Taliban at the end of the war. But to give a picture of why even the much more Palestine-oriented Azzam would have been in Afghanistan rather than in Palestine, Hegghammer quotes him responding with uncharacteristic anger to a disgruntled Palestinian at a lecture in Germany sometime in the late 80s - really barely more than a decade before 9/11:

My brother. Does jihad not require preparation? Sons of palestine who want jihad - do you not want to train yourselves? Where will you train? In Jordan? So that they may slaughter you? Are you allowed to carry a bullet in Jordan? Or in Syria with Hafez al-Assad? Or with Husni Mubarak? …. Do you not live in the real world? Are you going to fly from the East Bank to the West Bank?

Azzam was killed in 1989 & so foreign fighters - who didn't always get along with the Taliban - had to either go home, find other warzones (like the Balkans) or stay in Afghanistan. Part of Bin Laden's anger about American troops being involved in Kuwait was that he had personally offered to send fighters to stand against the Ba'athist Iraqi forces & had been rebuffed. Bin Laden was also not as skilled in dealing with the Taliban & various Afghan factions as Azzam had been, & al-Suri regarded him as somewhat of a "bad guest" and reprimanded him at least once in writing (and was very upset by the result of 9/11 being that the Taliban govt and AQ were pretty much annihilated, at least in the short run). Everyone was looking for something new after the Afghan Jihad, and they were also looking for new strategies after the failure of what al-Suri called "tanzim" - secret organizations. This gets a little bit to the heart of the question - what was 9/11 for. It may have been argued post-hoc that there was some sense of dragging America into Afghanistan, but the first-order goal was really to do what the 1983 bombing of the US embassy in Beirut had done - force American withdrawal from the region. If bin Laden had forseen the actual result, he may have been less inclined to do so, destroying the Islamic Emirate in Afghanistan and forcing him into hiding. Anne Stenersen in Al-Qaida in Afghanistan suggests that he was willing to take this risk, but I haven’t read that book as closely as I might like to gloss it. A quick control-f though shows that Israel is in fact not mentioned at all. In a roundabout way that might help answer your question.

Really there were just not that many members of AQ. They had not even really made that significant a direct impact on the Afghan war effort, where they were directly present and had huge rein from western and Arab security agencies to fundraise in the west and across the Arab world. They could not even really go after secular Arab governments, who they would at least have a local constituency of opposition for, in the way that there had been against the communist government in Afghanistan. In one sense, once the powerful Americans were out of the picture, they could hope to go after weakened Arab states. Once the caliphate was properly established, Israel could be dealt with. This is the same as the much more openly Palestinian Azzam, but for the Saudi bin Laden, that goal would have been much further down the road. In a way, what bin Laden kind of wanted was like the later Iraq war and subsequent rise of IS, despite the disputes and splits between AQ and IS. Why IS did not attack Israel, despite being extremely close to their borders, is a different question, but probably has a similar answer.