Mmmm, it'd be better to spread the attack out, and besides, given how the Capitol Building is THE most visible symbol of American political power, second only to the White House (which may have been too damn difficult to hit anyways), even if the attack itself killed nobody on the ground, the visual image and its symbolism would be just too good to pass up. From a propaganda perspective, what would be better? Two plumes of smoke billowing from the Pentagon (admittedly, that would be a better attack in terms of actually doing damage, and reconstruction would be a lot more time-consuming), or seeing the images of both the Capitol and the Pentagon in flames?
Besides being an extremely devastating attack in economic and human terms, this attack in particular, and terrorism in general, is also, if you will, a kind of political theater, as much for its symbolism as for its actual targets and such. The Twin Towers were chosen as the targets in New York because they fulfilled both the actual damage and the symbolic criteria, although the damage there went even beyond Bin Laden or Zawahiri's expectations. They were hoping at best to have a portion of the towers collapsed, or still on fire, which would have made recovery at the site even more difficult.
Coming back to the OP intent, I think, an even more devastating POD here would to simply have had Flight 93 and Flight 77 both take off on time (IIRC, 77 was not delayed long enough for the passengers to figure out what was happening on the ground). If the passengers on Flight 93 never had gotten those calls, or gotten them just miles outside of DC, there's nothing to stop the attack from going off completely as planned. On top of that, if the plane had impacted the Capitol Building before either the Pentagon or the South Tower was hit, that would actually kill a good number of Congressmen. Everything else that day as OTL, but a decent portion of Congress, House and Senate alike would have been taken out. The butterflies here would be massive. On the one hand, Congress itself would be even more in agreement on retaliation, and for that matter, much stronger retaliation (hit them that close to home, and no one in either party is going to object to even more stringent security, etc). The rest of the butterflies would depend on exactly who is killed/injured/in the building at the point of impact, but for the time being, the executive Branch would have more power and leeway to do whatever they wanted in retaliation.