I'm no more or less a fan of Nalgene, but one option you may be overlooking is using the Nalgene as something other than your primary water source. As primarily a carrying device, it leaves you with many options, nesting your cup, hard sided carry, water retrieval, etc. Also, there are many carry pouches that a Nalgene fits in, which gives you as many options for adding it to your kit.
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It's not that life is so short, it's that you're dead for so long.