I am deeply dubious about calls for massive overhauls of doctoral programs in the humanities. Not because doctoral programs are not in need of reform (anybody have a door to which we can nail some theses?), but because these calls seem to be missing the administrative forests for the departmental trees.
1. As Marc Bousquet has been reminding us all for goodness knows how long, we do not have too many Ph.D.s; we have too many t-t lines transformed into low-paying adjunct positions. (Or, as Claire Potter observes of the Stanford article, "The proposal says nothing about the role that Stanford, like every other university, has played in cutting tenure-track lines and in sitting on the sidelines while state legislatures and the federal government cut funding to state unis and community colleges.") Reworking graduate programs into training grounds for "alt-ac" careers does little to challenge the casualization process. If anything, it tacitly agrees that adjunct labor will be the new normal.
2. It is not immediately obvious to me that students who do not plan on going into academia will be best served by remaining in, say, a Ph.D. program in English. In an exchange I had with Michael Berube on Facebook, Michael noted that Ph.D.s who went on for careers related to higher education found a use for their doctorates--which is fine, except that many Ph.D.s will not be doing anything related to higher ed, and should probably be counseled out of their programs posthaste (and, quite possibly, into a program that might actually be of practical use to them).
3. The IHE article on Berube's speech notes in passing that "many graduate students only want to be professors." Surely this qualifies as a "well, yes"? If you had taken me aside in year two at the U of C and told me, "You know, you might want to think about a career in grant writing instead," I probably would have been more than a trifle irritated--I was in graduate school because I wanted to be an academic. Now, quite a few people decide along the way that they don't want to be academics after all, in which case see #2, but for most students, the purpose of struggling one's way through graduate school is an academic career.
4. More emphasis on pedagogy would be a good idea, but attempts to slot people into, in effect, "R1" and "teaching" graduate programs--a "a rigorous four-year master's program," as the CoHE report has it--is a terrible plan. Again, it's not clear what these alt-Ph.D. programs are intended to do, other than preserve the status quo of graduate enrollments in Ph.D. programs so that faculty still have teaching assistants (and graduate seminars to teach). One could, of course, suggest that some of the teaching currently being done by TAs be handed over to--wait for it--t-t faculty. (How about giving the composition programs some actual t-t lines, for instance, and not resting everything on the shoulders of lecturers, instructors, TAs, and part-timers?)
Incidentally, it is also perfectly possible to do research at a non-R1.
5. In my old age (OK, I'm 41, but I'm older than when I started teaching, right?), I have become increasingly grouchy about "interdisciplinarity" as a proposed solution to...well, any sort of problem, really. It's exceptionally difficult to learn how to do one discipline well. And once you've mastered that discipline, you tend to think in terms of its questions and methods. (Despite the reputation for being a historian that I've somehow acquired, I don't think like a historian; I think like a literary historian, which is not actually the same thing.) Interdisciplinary work at the dissertation level is very likely less interdisciplinary than it first appears, much like interdisciplinary work by senior faculty is also very likely less interdisciplinary than it first appears.
For the record, I finished my doctorate at the U of C in five years (I had one of the now-defunct five-year Mellon fellowships, and had no intention of outstaying my funding). I emerged from the program with no teaching experience to speak of, and while my dissertation was a good one, it was completed under the assumption that dissertations are there to finish, not to polish. It turned out that I was pretty much unemployable until I had notched a year of (really terrible--sorry, former students!) non t-t teaching on my figurative belt.