What you describe is typically how I use R. It certainly has it limits performance wise, but it is hard to beat as a "stat toolbox". Even in cases where it wasn't up to performance needs, I've found it useful for investigating which methods to use prior to implementing a full-blown solution.

For example, I used the free R package "earth" to confirm that something like MARS(Multivariate Adaptive Regression Splines) is a good approach to a particular analysis. For my client that initial test justified paying Salford Systems for their great, but expensive, CART/MARS software.