Matt Birchler does a deep dive on the various options for charging the Apple Pencil — how it currently works and what Apple could do in the future. And I think he came to the right conclusion in this one:

In 2018, I think the best option of the bunch is what Apple already did. The built in Lightning connector works in almost every situation and works across all devices the Apple Pencil is compatible with. It looks a little funky, but as a function over form decision, I think it was the right call.

The best alternate charging method I think is the Smart Connector idea. Now they would need to add a second connector to the iPad Pro, and the lower end iPad would just not have this option, but it would combine the relative reliability of a physical connection, use the device you have with you, and would look a heck of a lot nicer than the current method.