One thing that served me well, I think, was ambition. Even before I went to college, when I was first falling in love with philosophy, my goal was to solve it. I wanted my worldview to make sense, dammit, and not be full of contradictions and incoherencies and "we don't ask that question" moments. Most of the philosophers regarded as great (Leibniz, Russell, Lewis, etc.) were grand systematizers who attempted to have an answer to everything, and were not satisfied with paradoxes/contradictions/incoherencies/articles-of-faith anywhere. Alas, no one so far has been able to succeed at this ambition, but nevertheless I think I learned so much more, and came to beliefs that are so much better, because of it.
Why? Well, one reason (though probably not the only reason) is that it helped me prioritize. It helped me move on from interesting-but-not-that-important puzzles and go for the Big Questions. And go straight for the throat instead of lollygagging.
The experience of trying to construct a coherent, non-contradictory complete worldview, only to encounter some new problem or puzzle that brings it crashing down, repeatedly is perhaps analogous to the experience of trying to construct a hypothesis about how celestial bodies move, or how optics works, or something, that can accurately predict all the data from all your experiments.
I was in a terminal MA program, and that was very much the case. Entire courses were taught on the works of specific people, e.g. "David Lewis," and much of the focus was on exegesis of written works, ranging from the Greeks to the mid 20th century. There were certainly exceptions to this, but philosophology was very much alive and well where I was. I don't know how it is for PhD programs, and I'd bet it varies considerably.
There's a recent trend towards formal methods, and you've had some movements like experimental philosophy that have also deviated from these trends. I myself went into a psychology PhD program since I thought there'd be more tolerance for my empirical approach to philosophy there (I was correct), and because philosophology isn't my thing. I've noticed that almost all of the papers and work I deal with in philosophy was published in the last 30 years or so, with an emphasis on the past 15 years or so. But I'm an advocate of "exophilosophy": doing philosophy outside the formal academic setting of philosophy departments, so I have limited insight into the state of philosophy PhD programs proper.
Pirsig's remarks seem a bit pessimistic. I've seen plenty of dissertations or articles generated from philosophical work that are very argument-centric. I don't know what an exhaustive search of the literature would reveal, but people can and do succeed at focusing on doing philosophy and presenting arguments; there isn't some universal demand that everyone focus mostly on history. I'd like to hear from some people with more direct experience in these programs, though.