R in econ departments? According to my personal observation the majority of (prominent) economists prefer use Stata for their statistical analysis and Matlab for other mathematical work. SAS and Excel are also used (especially in finance). 

In my opinion R is a much better software for data cleaning, manipulation and analysis than Stata (not to mention that Stata costs) it is also seems on par with Matlab in what it does best. But I guess (as a graduate student) it will not make cooperation very smooth using a different statistical program than the rest. Use Stata like everyone else or suffer?

Thus a student who is an 'R expert' should, if having to choose between two equal departments, choose the one that uses R. But does such a department exist? A department where at least few researchers use R?
In my university the choice of
program is considered generally irrelevant. We focus on results, and it is up to each student to determine which program is best suited for the task and user preference.

You will find that using one language translates very well to another. With resources like stackoverflow, I would not be too concerned about which.

I would very carefully consider the statement "two equal universities". My experience has suggested to me such a thing does not exist, granting personal ambitions, career goals, and topic preference. I think programming choices are perhaps only a proxy for technical rigor and budget, little more.  Given you are only accepted to a finite number of schools, take time to evaluate this criteria closely.