So right now for Xbox 360 you need a special proprietary cable to charge your controller right? You can insert 2x Eneloop batteries and use the proprietary cable to charge them, but there's no way to use your own solution. With Xbox One you can use a standard non proprietary cable to connect to the Micro USB port in the controller to charge your batteries... am I missing something?
Yes you are missing something. You cannot charge Eneloop batteries while they're sitting in your 360 controller. It's just not designed to do that. The play and charge cable is only designed to charge the play and charge kit.