Personally, I just don't like the idea of rechargeable batteries that you can't swap. It puts you in one of two situations:
1). You are constantly charging the battery even when you haven't depleted it, just to be sure it is ready when you want it. This is horrible for the battery in most cases.
2). You charge the controller only when the battery is depleted, meaning you either have to play with a wire or have a second controller on hand.
The battery compartment facilitates the quick swap even if you opt to purchase battery packs.