Apple never touted the pencil charging via iPads as anything other than for quick top offs. I used it frequently and it worked well. The solution they have now is much better but that obviously wasn’t ready for gen 1.
I cannot deny what you say is true...I think what happens with so many things today, is that certain things go viral, become memes, have unintended consequences or the adverse effect is a consequence of the design. The design of the original Pencil constrained how it would be charged and while plugging it into the Lightning port of your iPad Pro was a convenient thing, there could be dire consequences should an accident occur. Is that bad design? No...but it is
a consequence of the design. Losing the cap from the pencil and/or the female to female coupler is a consequence of the design. The Pencil is beautiful design, as many thing Ive designed for Apple. I think my criticism would be that some of his designs, while gorgeous, worked in a less than stellar manner once the compromises of the real world began to intrude.
I have an iPad Pro 12.9-inch 1st Gen with an Apple Smart Keyboard. I love the keyboard itself, I type quite quickly with it, the fabric is not exemplary, but it is durable and if I spill a liquid, it is not shot to Hell. However, it is dark grey and does not have the best contrast in low light situations, as Apple (or Jony) opted not to put any sort of backlighting in it. A consequence of the spill proof design, I would reckon. But it also has no media keys or shortcut keys, which I think were left off because Design thought they were too gauche or offended Jony's sensibilities, I don't know. However, dealing with the lack of backlighting and reaching up to press the Volume Up or Down on the top left of the iPad Pro soon became rather tedious and ultimately I snagged the exact same Logitech Slim Combo I initially ordered for my wife's iPad Pro 12.9-inch 2nd Gen. Does it look as good as the Apple Smart Keyboard and Silicone Case combo I previously had? No. Does it work better on a day in, day out basis? A resounding YES. While not spill proof, the backlighting and shortcut keys make my work life loads better and more productive. No more reaching up to control volume, I simply hit the volume button on the keyboard and keep on typing, which means one less "mode" change. The same for the Home button and the Lock shortcut buttons on the keyboard.
While Apple pursued form (aesthetics) or function (not nearly as nice looking), it seemed as though the practicality of Jony's quest became less and less realistic as time went by. And for a while there was a balance, but in the past few years it has veered too far to the form side.
For instance, I love my 2016 15" MacBook Pro...I love the slim chassis...but the consequence of that is the battery is smaller and just doesn't last as long, annoyingly so in any sort of sustained workload. They butterfly keys are beautiful to look at, but unforgiving if your typing rhythm becomes disrupted as they really want to be struck perfectly dead center. The keys are placed closer than they are on the Magic Keyboard II or on the 2012-2015 15" MacBook Pro keyboard and its just enough to make typing more awkward than it needs to be. And that seems to be because not only did Jony want the 15" MacBook Pro thinner, he wanted it smaller (LxW) and typing on it just isn't as satisfying as typing on just about any other keyboard on the planet. The 2015 MacBook being the most extreme example. Here is a short excerpt from a review of the 2017 12" MacBook.
I think all of these and many other things over a period starting in 2012 up until now culminated with Ive's departure. Sure, it coincides with Steve's death, but it also seems like Ive needed a tether to reality and no one individual at Apple could command Jony's respect to be that tether. It may not bode well for his new design agency.
A great era has come and gone and now a new era begins...it will be interesting to see how it proceeds.