As you mentioned, there are pros and cons to inventing the Stan DSL. Originally, we wanted a language that was not too different from the BUGS language because the BUGS family was what most applied Bayesians were using (if they weren't using some specialized MCMC algorithm for their problem).

And programmatic manipulation (while not impossible) of a Stan program was not high on our priority list. Since the underlying language is C++, you can bypass the Stan language and write (or generate) the C++ directly with a lot of effort. It uses standard (including Eigen) data structures.