Aluminum bottles are a non-starter: aluminum is toxic to humans, and has to be coated to not leak into your food. Often times there's a plastic liner to prevent the aluminum from coming into contact with your food/drink.
Some steel bottles are crap: they actually do stain/rust, and being non-transparent this can be hard to spot.
Glass bottles are nice, but obviously more breakable/dangerous than metal.
Personally, I don't trust any plastic bottles: not Nalgene not any other kind. Had a Nalgene bottle once; after it took on a stale water odor, I could not get it out with anything. This article particular finding is far from the last one in terms of which plastics do what to the organism.
For baby bottles... I guess the search is on for the next best type of bottle.