Letting the water sit is a good idea, but if it doesnt get any sunlight, or extreme heat, it wont make the water any better/safer for your reptiles. As for the filtration systems, that does seem like a much better/more efficient method to de-mineralize the water.
As for the plastic waste, I know my local exotic pet store offers a discount for reusing containers, as well as a bulk discount for something like 10+ gallons at a time. I know some people use big 10 and 20 gallon "Culligan" bottles and 5 gallon buckets. Buckets are nice because they can be left in the sun with enough surface area to do some good, whereas the bottlenecked containers like Culligan bottles are pretty much useless for sun-safing water since the plastic absorbs most of the UV light.