IMO, 9/11 was far worse in that it was staged via murder, and attacked a soft target of civilians for the most part. As Hijinx said, the US military and govt had a pretty good look at very possible attacks on US military installations in the Pacific, and just sat on their hands waiting for it to unfold vs not knowing it was coming. There were hints that something was going down prior to 9/11, but the Gorelick Wall prevented agencies from connecting the dots. Both attacks result from the very top level of govt (FDR because he just wanted to do nothing, Bush could do nothing because of the walls set up by the Clinton presidency and Gorelick) doing nothing to try and stop them from occurring.
MY opinion based on historical evidence.