You will find that when you need a quick charge, inserting Pencil into IPP is a really great thing! 15 seconds gives you quite a bit of battery. I got over the "looks funny" issue the first time I tried it.
This.
The design reason for this seems obvious and simple to me: Apple wants people to be able to charge this thing both at your desk, and away from it. If it was a female plug on the Pencil, so it would just accept a lightning cable, you could charge at your desk just fine, but then you need to remember to bring the charging cable and brick with you.
The way it is designed, the workflow actually makes a ton of sense:
- If I am at my desk, I can charge the iPad or the Pencil from the lightning cable, using the supplied adapter.
- If I am in a meeting, the only things I need to bring with me are the iPad and Pencil itself. The iPad should easily survive a 1-2hr meeting (I only charge at night), and if you do get caught with the Pencil's charge low, you can just plug it in for a quick boost to get through the meeting.
It actually makes it less likely for you to lose something by forgetting it at the meeting, since you take less stuff with you when you get up from your desk. To me, that's the right way to do it.