A few observations.
1. It is possible for a group of helos to fly low and fast and evade the radar for most of the distance to reach abbotabad.
Add to this the fact that these helos probably had stealth features, RAM coatings, possibly radar evading shaping. For silencing, the rotor blades were shaped at the tips (like in the EH-101s and the Silent Hawk pictures that we've seen).
The reason why it is possible to fly from Bagram to Abbottabad undetected is because there is no major airbase in the hills there, and consequently no radar stations there.

The major airbases west to east are along a line at the foot hills, and they are Peshawar, Risalpur, Kamra, Chaklala.
There are Radar sites are in Peshawar, Cherat Hills, Risalpur, Kamra, Chaklala (Islamabad). The radar on top of Cherat Hills would be the big daddy long ranged one, keeping an eye over the entire area. The rest of the major radar sites are at Sakesar, Kallar Kahar and Kirana Hills, and are way south of this area.
Again these radar sites are intended to provide cover for the eastern sector aimed at India, and will have major blind spots looking north-west. Perhaps only the Cherat Hills radar, and the Kamra AFB radar would look north and west at the Af-Pak border area. Once the hills start up north, there are several blind spots in the valleys, and because of the earth's curvature, the line of sight gets disrupted.

The white arrows mark the areas where the hills begin in the north. The area north of this has numerous valleys and hills - ideal for low flying aircraft to disappear into.
One more thing about Pakistan's Radars. I wonder if a technically superior military power like the US which would know both frequencies and algorithms of pakistani radar could jam them in a very specific manner so that they would just be blind in certain directions, and the Pakistanis wouldn't suspect anything. Usually indiscriminate jamming of all frequencies leaves several artifacts on the radar screen - although the radar is jammed, but the defenders are aware that the radar has been jammed. Any experts want to pitch in here? As it is, most of these Radars are US / Western supplied ones, except the chinese ones with the SAMs.
2. Pakistan has F-16s armed with BVR AIM 120 missiles based at PAF Mushaf, Sargodha, which is about 240 Kms from Abbottabad, and about 300 Kms from the Af-Pak border around Jalalabad.
I don't expect that these F-16s would have been capable of intercepting, much less approaching american aircraft.
There was no way the PAF would dare to take on the USAF, when they don't even dare to take on pilotless drones!
Pakistan has an HQ-2 SAM site east of Rawalpindi, but again that would not have been able to track or target the helos up north.
3. I am sure that the US had an AWACS up in the air and that too well within Pakistani Airspace, in addition to fighter aircraft equipped with both air to air and ground attack ordinance in separate groups.
Any commando raid these days, and specially one of such magnitude would probably have a live UAV SAR mode feed, back to the command area in Bagram and in Pentagon. It is possible that there would be multiple UAVs in the Air.
4. I don't think that the US has to stoop so low so that the POTUS has to threaten Nuclear attack to a puny military adversary like Pakistan!
I don't think that an overt nuclear threat was made in so many words. There is no reason to not believe John Brennan and Leon Panetta when they say that Pakistan was informed only once the US forces were out of Pakistani air space.
Halfway through the raid, the Pakistani military leadership must have been informed that the area around Kakul, and later on that, the area around OBL's safehouse was under attack, and there were helicopters in the air. They must have realized that the US has attacked that site. Since India wouldn't attack out of the blue, and an air raid meant that OBL's other enemies (and there are groups who would love to see OBL dead - the northern alliance for example) wouldn't have access to aircraft.
The US would have gotten in touch with the Pakistanis:
Chairman, Joint Chiefs of staff - Pakistani COAS
CIA chief - ISI chief
US Ambassador - Geelani and Zardari (The next morning)
To inform them about the action.
5. Hyperspectral Imagers? Wouldn't that have told the SEALs that a six foot tall figure seems to be present on the third floor in such and such room?
I think that the initial landing party landed on stealth and 'reduced noise' helos at several spots on the compound - the roof of the main building and the ground around it and on top of the outhouse. The team on the roof did a top down approach, the team on the compound went into the building making its way upstairs, and one team took out the outhouse, where they came under fire and they promptly killed both OBL's courier and his wife. If there was a lookout in the compound who was visible, he would have been taken out well before the team landed.
There would have to be another team to do the cordon, and helos in the air to help enforce the cordon. The initial raid would be silent and swift, and would most likely have been over in a few minutes, the numbers being thrown about 3 -5 minutes seems about right. This is because there was no resistance at all except the man in the outhouse who managed to fire some rounds off. OBL was taken out probably by the time the man in the outhouse was firing the rounds.
6. Local residents mention a few things:
a) There was a power cut at that time - That town is undergoing power cuts like every other pakistani town for about 10-12 hours every day or more! The CIA team on the ground would have a good idea of the times of the power cuts in that area.
b) The locals heard several helicopters buzzing low overhead. One individual describes hearing 4 low intensity bangs in quick succession followed by one big bang. Probably the helo being destroyed with explosives and the fuel tank blowing up in the end.
c) No one describes the sound of gunfire! Probably because the SEALS had silenced weapons, and the guard only managed to fire a few rounds.
d) There was no Pakistani army or local police on the site until after the attack was over! There are several individuals corroborating this fact. In fact, true to form the Pakistani police was the last to arrive, and they found a Pak Army cordon in place when they arrived.
One can just imagine the scenes in PMA Kakul when helos and explosions were going off just outside the perimeter. Utter confusion must have reigned, and people must have been running helter skelter all over the place. The security must have first tried to ascertain if the PMA itself was under attack, and so a team would have had to go in the general direction of the noise along the perimeter wall. They would also have rushed teams to secure the GOC, and senior officer's residences, and rushed teams all around the perimeter and guards around the Gentleman Cadet Hostels.
One wonders if they would have been able to mount an effective raiding party to take out 70-80 odd NVG equipped US Navy Seals in the middle of the night - and that too in 40 odd minutes!
The SEALs initial concern probably was to remain undetected until the first shot was fired, they probably had a good idea of Pakistan's response times, and they planned to be long gone before the pakistanis could mobilize. The operation itself turned out to be a cakewalk it seems.