Rechargeable AA batteries are a thing. From an ecological point of view, the custom battery is a bigger problem. In 20 years the controller will still work and AA batteries will still be available, but no one will be making new built-in rechargeable battery replacements (even if Valve originally intended for the battery to be replaceable).
One of my favourite controllers has been the Dual shock controller. I've got 2 PS3 controllers that I love using. Their rechargeable batteries are shot to shit. I would be much happier if I could use AA.