They're one coup away from a nuclear-armed and unapologetically pro al Qaeda regime that could trash Afghanistan, re-start the Kashmir war with India, and provoke China into God knows what. Invading and subjugating such a nation is probably impossible and would require the cooperation of nearly the whole world.
The news from Pakistan is a Le Carré mess of garbled signals and spooky tidbits. It's pretty clear from everything you can see that bin Laden and Omar live there and are protected, that their "tribal areas" are not in any way governed, and that Musharraf is the classic doomed dictator trying to play both sides of a losing game.
And nukes. If Seymour Hersh is to be believed, Bush Sr. just barely kept Pakistan from attacking India with nuclear weapons during a particularly bad time in those two countries' relations. Personally I'd much rather worry about a nuclear Iran than about a place that's barely a nation and dominated by mobs and "tribes" owning nukes and F-16s.
I wonder how much bourbon they go through in the Pentagon when they play out these scenarios.