the potential for botched operations that fuel anti-American rage; a blurring of the lines between soldiers and spies that could put troops at risk of being denied Geneva Convention protections; a weakening of the Congressional oversight system put in place to prevent abuses by America’s secret operatives; and a reliance on authoritarian foreign leaders and surrogates with sometimes murky loyalties.

Then there's the blending of functions:

The administration’s demands have accelerated a transformation of the C.I.A. into a paramilitary organization as much as a spying agency, which some critics worry could lower the threshold for future quasi-military operations.

The Times asks who should be running this covert/shadow war. Using an example of a strike in Yemen, it says:

The Yemen operation has raised a broader question: who should be running the shadow war? White House officials are debating whether the C.I.A. should take over the Yemen campaign as a “covert action,” which would allow the United States to carry out operations even without the approval of Yemen’s government. By law, covert action programs require presidential authorization and formal notification to the Congressional intelligence committees. No such requirements apply to the military’s so-called Special Access Programs, like the Yemen strikes.

There's also questions as to whether the shadow war is having the desired effect. AQAP, for one, is not any weaker.

Despite the airstrike campaign, the leadership of Al Qaeda in the Arabian Peninsula survives, and there is little sign the group is much weaker.

Attacks by Qaeda militants in Yemen have picked up again, with several deadly assaults on Yemeni army convoys in recent weeks. Al Qaeda’s Yemen branch has managed to put out its first English-language online magazine, Inspire, complete with bomb-making instructions. Intelligence officials believe that Samir Khan, a 24-year-old American who arrived from North Carolina last year, played a major role in producing the slick publication.

The operative question:

Do the selective hits make the United States safer by eliminating terrorists? Or do they help the terrorist network frame its violence as a heroic religious struggle against American aggression, recruiting new operatives for the enemy?

Seems pretty clear to me the second option is the correct answer.

A former Ambassador to Yemen points out the U.S. can't rely solely on the use of force.

Edmund J. Hull, the United States ambassador to Yemen from 2001 to 2004, cautioned that American policy must not be limited to using force against Al Qaeda.

“I think it’s both understandable and defensible for the Obama administration to pursue aggressive counterterrorism operations,” Mr. Hull said. But he added: “I’m concerned that counterterrorism is defined as an intelligence and military program. To be successful in the long run, we have to take a far broader approach that emphasizes political, social and economic forces.”

Obama officials respond:

They emphasized that the core of the American effort was not the strikes but training for elite Yemeni units, providing equipment and sharing intelligence to support Yemeni sweeps against Al Qaeda.

I'm not seeing any social and economic help to the people of Yemen in that answer. What's next, are we going to go in and destroy their qat crops, claiming it's contributing to terrorism and draining their water supply?

Instead of ramping up military strikes we should be providing developmental aid. As Gregory Johnson, a former Fullbright scholar now at Princeton, and co-author of the Yemen blog, Waq al-Waq, wrote last year:

The US and other European and western countries cannot afford to focus on the al-Qaeda threat in Yemen to the exclusion of every other challenge. There has to be a holistic approach and an understanding that all of the crises in Yemen exacerbate and play-off against each other.

Simply targeting the organization with military strikes cannot defeat al-Qaeda. Something has to be done to bring a political solution to both the al-Huthi conflict as well as the threat of secession in the south. Not dealing with these will only open up more space for al-Qaeda to operate in as well as creating an environment of chaos and instability that will play into the organization’s strength.

Indeed, by focusing so exclusively on al-Qaeda and by viewing Yemen only through the prism of counter-terrorism the US has induced exactly the same type of results it is hoping to avoid. This demands much more development aid to the country as a way of dealing with local grievances in an attempt to peel-off would-be members of al-Qaeda.

If we don't help Yemen with its economic issues, the war on terror won't be much of a help. Yemen's problems won't stay within Yemen.

Military operations to kill or capture al Qaeda operatives will likely increase in 2010. These actions carry risks. Publicly acknowledged American involvement in counterterrorism operations in Yemen would be deeply unpopular in the country, likely undermine the legitimacy of the Yemeni government and feed into the grievances that help fuel al Qaeda militancy.

Development assistance is one of the most effective tools available to address the interconnected long-term challenges facing Yemen. But, U.S. aid is disproportionately small considering the magnitude of the problems facing the country and Yemen's strategic importance to the United States.

Here's more, quoting another analysis by Gregory Johnson (pages 8 -11):

The United States must learn that its insistence on seeing everything through the prism of counterterrorism has helped to induce exactly the type of results it is hoping to avoid. By focusing on al-Qa`ida to the exclusion of nearly every other challenge, and by linking almost all of its aid to this single issue, the United States has ensured that the issue will never be resolved

...This short-sighted and narrow focus by the United States has translated over time into a lack of influence within the country. The United States is not the most important player on the domestic Yemeni scene.

I'll bet I'm not the only one disappointed that when it comes to the war on terror, Obama's vision and focus seems as narrow and misguided as that of his predecessor.