President Bush is careful to speak of the "greater Middle East," to include countries not historically considered part of the Middle East. Pakistan and Afghanistan are generally considered to be in South Asia, not the Middle East.
Remember the old CENTO treaty? Central Treaty Organization which succeeded the Baghdad Pact. Iraq, Pakistan, Turkey, Iran, UK and US.
The reference to Israel as having "the Middle East's only nuclear arsenal" insinuates that Israel is consequently the real source of instability in the region. In that context it is disingenuous to exclude Iran, for example, or Pakistan (from which nuclear knowhow has been exported to Iran), particularly when many people would consider them part of the region.