Back then Apple didn't have much experience with wireless charging. They also didn't have any place to "dock" the pencil to the iPad, even though other companies were using magnets. So that seemed like an explicit decision at the time to me.
I saw a video where artists were demoing the iPad Pro Photoshop. Most of them had experience with the Wacom stylus and criticized that the Apple Pencil was too slim and cramped their hand. The obvious solution would be to add a rubber grip--which wouldn't really work with this storage/charging solution.
Could have made the Pencil triangular. The new shape fixes yet another annoying ergonomic issue with the original - that it's really hard to hold comfortably for extended period of time. There's a reason pencils are hexagon, and pens have rubber grips.
I don't know why the pencil didn't come with magnetic attachment from the get go, it seems like such a simple change that makes a big difference.
The cynic in me thinks that it was deliberately withheld in v1 so that a big deal about its addition could be made in v2.