Hakeemullah Mahsud has always been the biggest threat but I will not discount the raw fanaticism of the Tariq Afridi group. They have continually kidnapped businessmen, slaughtered Sikhs... there are also rumors that their faction in conjunction with Hakeemullah Mahsud is responsible for the kidnapping of doctors from the city of Peshawar. Tariq Afridi's militants constantly move in and out of Peshawar and there is evidence that Hakeemullah outsources some of his dirty laundry to Tariq Afridi.
We cannot discount the other Taliban groups because they are in reality allied to the TTP and like Hakeemullah Mahsud we haven't been able to hunt their commanders.
It is pathetic that in all this time we have not managed to take out a single commander. Mullah Toofan still active in Kurram despite operations in his area of influence, Faqir Mohammad active despite operation Janbaz in bajur, Omar Khalid still operates in Mohmand. We are so pathetic we couldn't get a single one of these commanders. Even failed to get Fazlullah from Swat (though the militaries performance in Swat was much better)
You are correct in your assessment, but I did admit that the other TTP factions & militant groups are threats to Pakistan (although not as severe as Hakeemullah Masood TTP faction). There is evidence that the TTP leadership has split badly, Wali ur Rehman & Faqir Mohammad make it to the list as well. The group has splintered into factions, each faction poses a certain threat to the Pakistani establishment, but as long as they can be made to fight & kill each other without the Army wasting a single bullet, they won't be as critical as the Hakeemullah Mehsud TTP faction.