[Clarke] thinks going to such a heightened level of alert and concerted effort in 2001 might have shaken loose much earlier the information that the CIA knew that Khalid al-Mihdhar and Nawaf al-Hazmi were in the US. As it is, the INS wasn't informed of this advent and did not start looking for them until Aug. 21, 2001, by which time it was too late. Since they made their plane reservations for September 11 under their own names, names known to the USG, a heightened level of alert might have allowed the FBI to spot them.
So it just is not true that Bush was doing exactly the same thing on terrorism that Clinton was. He didn't have a cabinet-level counter-terrorism czar; he didn't have the routine of principals' meetings on terrorism; he didn't authorize Clarke to go to 'battle stations' and heightened security alert in summer of 2001 the way Clinton had done in December, 1999.
The second point is that the Bush Administration was too focused on state sponsorship of terror as opposed to recognizing Al Qaeda as an independent actor. The difference is critical - Fareed Zakaria explains the difference in a great Newsweek article. Kevin Drum also reminds us "a senior Bush State Department official told CNN the U.S. government made a mistake in focusing so much energy on bin Laden."