It's a decision of product proposition, and Apple decided that the Pencil use-case shall support iPad sales and not be cannibalized by the iPhone.
They also decided for a while that all their premium iPhones shall have "Force Touch", an entirely unique display technology only for iPhones to sense pressure without the potential of additional accessory sales.
These are all valid decisions. They are not a charity, they operate to maximize the profit they can gain from each customer.
The iPad has the big "issue" of barely needing to be replaced with new models, as most use-cases are consumption-oriented and there are no real disrupting sales-driving requirements for iPad media consumption.
So the Pencil was created to drive the proposition towards Media CREATION, because people would buy a new, more-expensive iPad then and requirements for that segment are constantly increasing (better pencils, lower latency, more-demanding apps).
Also in the past year: iPhone increases focus on Media recording with more-complex video features, iPad is tagging along with demanding Media processing use-cases