The nice thing about the whites is if you have the maps and can read contour lines you can modify your trip on the fly. AMCs shuttles are oriented to the needs of hut visitors but they do run from the big three notches, Pinkham (RT 16), Crawford (rt 302) and Franconia (I 93). I expect few folks would voluntarily skip the presidential ridge between Pinkham and Crawford Notch. One shortcut is to drop down Crawford Path directly to RT 302 (Highland Center and take the AtoZ trail to Zealand hut this cuts out one day, about 2/3rd woods walking through an area (ethan Pond to Thoreau Falls that can be wet in June. Then at Guyot the option of going out the Bonds to Lincoln is available as well as dropping down to Thirteen falls and out via the Pemi from Galehead in place of the Lafayette ridge if the forecast is marginal when you stop by Galehead.
AMC costs a lot less than the Shuttle Connection and many other private shuttle firms but the trade off is time on trail and money. If you want to maximize time on trail use a private shuttle. if you dont mind losing a day on either end of the trip use the AMC.
As for conditioning, the PCT is setup as horsepacking trail in Oregon and is set up with switchbacks and sidehilling, granted you may cover as much elevation in a day on the PCT, but it is lot more gradual. As a visitor from out west commented once when seeing Webster Cliff trail (the AT) in Crawford Notch" if this trail was out west it would be closed off with yellow safety tape as being a rockslide". There are no switchbacks and almost no sidehill in the whites on the AT and very little elsewhere (the south face of Bondcliff and the Osseo trail are exceptions). The rocks of PA, NJ and NY are a PITA due to footing issues but the only spot in PA that resembles much of the AT in the whites is the Northbound climb up from Lehigh Gap through the area that was denuded by a smelter. In some spots, in the whites, this type of terrain can go on for 1000 feet vertical. Sure fit folks can and do long days right out of the box but many dont and end up changing their plans. Heck even thru hikers complain about the climb up from Pinkham to the top of Wildcat.