The main point being that magic systems in RPGs are too "scientific". In my mind, this means logical and reproducible. To some extent, I agree... in fiction, I really appreciate when magic comes across as something not wholly explainable and mysterious. "A Game of Thrones" by George. R. R. Martin, and "Jonathan Strange and Mr Norrell" by Susanna Clarke are two examples that spring immediately to mind.
However, to make this actionable in a CRPG (the author is primarily talking about pencil-and-paper RPGs) is difficult, and not really addressed by the article. By definition, a computer game is running a set of logical rules to define the magic system. The implementer can add randomness to make things non-deterministic, but to fool the player into believing that this randomness is synergistic and mysterious, rather than just random, is a tall order.
Anyways, food for thought, but I can't think of much to actually do about it. Anyone else?