A few days ago, CNN had an article about how various militant groups in AfPak were putting aside their differences, at least temporarily, to fight NATO:
The next day, another article comes out saying that the Taliban are willing to engage in talks with the NATO occupiers:http://edition.cnn.com/2012/01/03/world/asia/afghanistan-taliban-talks/index.html?hpt=hp_t3
My question: How did ISI pull this off?
The Haqqani network, the Pakistani Taliban, the Afghan Taliban (the distinction between the latter two being quite blurred), and "associated jihadist groups" don't just set aside differences one day. That feat requires organization, a shared goal, and a forum where the different sides can discuss tactics and strategy to achieve their stated goals. There is really no other venue to do that besides Pakistan, and there is no other entity capable of arranging this beside the ISI.
A unified front of militants presents several advantages to all involved. First, tactically, having the entire AfPak border region working towards the same goal is beneficial because it allows coordinated strikes, greater areas of refuge for retreat or re-grouping, shared intelligence, and a possible pooling of resources (though pooling of resources is unlikely, as it's bad long-term strategy. After all, why give your potential future rivals arms to later use against you?)
Second, strategically, coordination gives a degree of legitimacy to the militants. It shows that these are not selfish fighters who are looking out for their own interests. Instead announcing their intention to work together is a great PR move, as they can now portray themselves as having sacrifised their own goals for the greater good. A sort of non-morbid militant martyrdom, if you will. Also, a council of elders can serve as a shadow government, further enhancing legitimacy, and as a possible negotiating party. If the Taliban and their allies intend on negotiating, as presented in the second article, the council of elders, in a sense, rightfully represents the interests of the militant networks in the AfPak region.
All of this is not necessarily good news for NATO. Having one enemy might seem preferable, however, having multiple enemies means that NATO can play one off the other in a classic move of divide and conquer. However, that strategy is not out of play with these developments. In fact, it becomes more lucrative. If there are formal networks of cooperation and a sharing of information between groups, those networks of information can be exploited more effectively and with greater payoff.
Returning to the original question, ISI likely is playing a dominant role in these negotiations and coordinations. What do they gain? Firstly, a measure of control over the entire region which they did not formerly have. Second, the ability to arm and direct militants in order to more effectively combat NATO. Lastly, they gain a bargaining chip with NATO. If they have the only phone line open to Mullah Omar, the US and NATO are going to have to rely on them to keep the line open. I'm sure they won't make the same mistake with Mullah Omar that they did with Bin Laden. I'm sure this time, instead of hiding Omar in a military garrison town, he will remain in the border region, well protected by ISI, but far enough away so that if caught, ISI can claim ignorance.