For the Magic Keyboard, yes, that is the main difference. It can also be used wired rather than wireless with the Lightning cable, and its keys are shallower and larger than the ones on the traditional Wireless Keyboard.
For the Magic Trackpad 2, the main difference is that it's now Force Touch, just like the newer Retina MacBook Pros and the Retina MacBook. Also rechargeable of course, and it requires OS X El Capitan and Bluetooth 4.0.
For the Magic Mouse 2, I believe the *only* difference is that it's rechargeable.