R in econ departments?
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.