I thought it a good idea to post this review as it was difficult to find much about this before we went. The Quarry Trail is an alternative offered by Intrepid Tours if there are no more Inca Trail permits available. Hopefully this will be useful to anyone considering this option.
First of all, if you are worried that this won't be a fantastic experience compared to the 'classic' Inca Trail, then don't be! We were really disappointed we couldn't get permits and the way Intrepid sells this option as a second prize is really misleading. The trail was by far the highlight of our time in Peru, and from talking to others we met who had done the 'classic' trail, much better in a number of ways.
Isolation. Myself and my partner were the only people undertaking the tour and we found ourselves the only 'gringos' as far as the eye could see (and probably further). We visited several Inca sites along the way and had them all to ourselves -- the only other people we encountered were local villagers going about their daily lives. After spending time in bustling Cusco this was fantastic.
The scenery. From start to finish the trail had spectacular views. The second night camp site was a highlight, waking up to the view of Mount Veronika above and the sacred valley below. If you are interested in photography (as I am) you'll be very happy. Again, the lack of other trekkers meant we could take our time with the views with no disturbance. Here is a small selection of shots along the way: http://www.flickr.com/photos/23250291@N03/sets/72157629690217988/
Intrepid staff. Our guide Yieber (Jeffersen) was the best guide we've had on any trip before. He even met up with us on his day off in Cusco to help us buy sandles, books and pens for the children we met (and carried them up the next time he went). The rest of the team (Ballentine, Emilio and Adrian) were also outstanding. Just like the classic tour, great food, morning coffee, the works. Intrepid seems to look after their staff very well.
Banyos. We heard some horror stories of toilets on the 'classic' trail. On the Quarry trail the team set up a little portable toilet tent at each camp site.
Quechuan village encounters. Our longest day happened on a Sunday and we came across several local children playing in their villages. Our chef supplied us with heaps of fruit every morning which was handy for us to give out. One one occasion we were invited into one of their homes which was a fantastic and eye opening experience.
Physically challenging. Being competitive people, we worried the trek would not be as challenging as the 'classic' trail. Hard to compare without having done it, but we found this trail to be challenging while not being overwhelming. It goes higher (4500m) so the altitude plays a part in adding some extra difficulty.
Staying in Aguas Calientes. I thought this part of the tour was a bit of a cop-out at first, but in the end really glad we stayed here the night before hitting Machu Picchu for hot showers and a good nights sleep. We saw heaps of broken people finishing the 'classic' trail heading straight for the busses and skipping the site altogether.
No hiking through cloud forests. While the scenery of the Quarry Trail was spectacular, it wasn't as varied as you'd find on the 'classic' trail.
Not seeing the sun rise over Machu Picchu. I can imagine this would be a fantastic sight and great feeling at the end of your trek. You do get up there early if you catch the first bus, but still, probably not quite the same.
That's it! Hopefully helpful to future trekkers wanting to know a little more about this option. If you're on the fence, then go, you won't regret it.