I find many instances where I recommend one over the other. I like helping out around here because much of the community is new at this and very passionate, and a great part of what WikiEd is about is training people on real wiki skills (there's nothing like Learning4Content that i've seen anywhere else!) - where people use those skills is ultimately irrelevant; and, Wikied is also more able to innovate technically, which is a major point of difference for me; but funnily enough I mostly like working on my own resources/projects on Wikiversity as it seems more akin to the type of projects that I'm particularly interested in using a wiki for, and I like at times interacting with skilled and experienced wiki users.
Take a look at this as well though: http://www.wikieducator.org/images/f/f6/WE_Survey_04262008.pdf it might provide an nice view of how different are the two communities. The diversity of the different projects will ultimately be a strength to the movement as a whole and we should I think cross-promote and cross-pollinate as much as we can. When this licensing thing is fixed i reckon it will open a flood gate of interoperability, reusability, and collaboration between the sites, and perhaps what this movement is edging towards: that the whole will suddenly be much greater than the sum of its parts will be that much closer. I nearly quit Wikiversity because of some of the ridiculous accusations of paranoid partisanship that were levied against me when I applied for Custodianship and i'm still somewhat wary of the effect of users on the site that are overly active in organisation rather than in creating valuable content/projects. Wikiversity is in my opinion desperately in need of some new and exciting projects - the OER course was the last one I can think of that had any real substance to it (and should be run again in an improved form i'd say.)
From my perspective WV and WE are "two leaves on the same tree" to cite Country Mike. I also think that there is considerable value in comparing and evaluating our collective experiences. WE has learned a lot from the WMF projects and we try to learn from these experiences. For example -- I was very surprised to see the productivity of the WE community comparing the ratio of pages to registered users.
We've been pretty successful in extending our work in the developing world and as Brent has pointed out, a lot of energy goes into capacity development in using MW technology.
For those interested -- you can view our daily stats here:
Ultimately the diversity in our OER projects will contribute to a better world for all involved.