If they had hit Los Angeles, especially some cultural or entertainment centre, it would have lent credibitlity to the whole "They hate us for our free-wheeling liberal culture" thing that was being pushed in the period after 9/11. IOTL, that line never really sounded entirely believable when you considered that Wall Street, the Pentagon, and the White House(especially under Bush) aren't generally considered bastions of social liberalism. Hollywood and the music industry, on the other hand...
And it would be interesting to have seen the impact on the national psyche of hitting some more identifiably liberal target. In real life, a few high-profile evangleicals got caught saying stuff like "Well, this is just America being punished for her decades of immoral hedonism." There probably would have been a lot more of those sort of "wacko eruptions" if the planes had hit Hollywood or, even "better", San Francisco.
(And yes, I realize NYC is generally regarded as liberal and cosmopolitan, but that aspect of its character was somewhat muted, in terms of interpreting the meaning of 9/11, by the choice of the WTC as the specific target.)