I have used the Nalgene soft cantene in the 32 ounce, 48 ounce and 96 ounce sizes. I have also used the Platypus bags in the 1 liter, 2+ liter, 3 liter and 4 liter ‘big zip’ reservoir sizes. Some of them I have had for years. Both have their pros and cons.
The Nalgene bags work well with the MSR water filter as they screw right into the bottom, but the wide mouth can be hard on the back if used as a hydration bladder in your pack. The Platypus bags have a smaller opening so it is easier on your back when used as a hydration bladder, but can be a little more difficult when chemically treating
For carrying water to the campsite, I prefer either the 96 ounce Nalgene bag or the 4 liter big zip Platypus. I like to make as few water trips as possible once camp is set. Both have a large opening for filling and can make it easier when chemically treating. If I bring my MSR Filter, I prefer the Nalgene bag. Both work well with an H2O Amigo gravity filter, but the smaller Platypus bags may take a little more care with the gravity filter.
Another thing to consider is the time of year. In winter camping, the smaller opening of the Platypus can freeze shut faster than the wider opening of the Nalgene.
There is a thread in Food, Hydration and Nutrition that shows a Nalgene Cantene where the top is replaced with an Aqua Mira filter and squeeze cap for a compact water bottle with filter included. I suspect you could use a straw filter with a Platypus bag.
I have read a recent thread on ‘Pee Bottle’ in one of the posts on this site and I must admit, it has shed light on yet another use the Nalgene is more adaptable for compared to the Platypus.
IMHO, I believe the biggest advantage of the soft side water bottles (bags) offered by both Nalgene and Platypus is the ability to provide the opportunity to carry bulk water storage in a more compact and lighter manner when not in use.