I can't stand the water bags. Too hard to monitor intake, freeze up on you in cold weather, prone to breaking, can't be screwed into a filter.
Not super big fan of Nalgene either, to be honest. Usually though, I have 2 in my pack. Yup, they work with many filters, but you can always just hold the filter and squirt the water in.
I also have a USGI on my pack's hip band. This way I can monitor how much I'm drinking, it's right at hand, I like the size/shape, and I can refill from the Nalgenes. Admittedly, a bit difficult cuz of the small mouth.
But the 2+1 bottle combo has worked for 20 years for me. The camelback bags sit in the bottom of my closet... though I like some of their bags (not their prices though)