In my experience, RPy is annoying to get working, because you're dealing with Python versions and R versions together. It's brittle and usually unnecessary, as it's you can just serialize to CSV or JSON.
If you can get away with using a single language that's good, and Python is probably the only one where that is possible (i.e. can write both prototype and production code, and data ingestion and machine learning). But I often have to use C++ because of the data size, and I think R's plotting is more convenient than anything in Python now.
The shell scripts have their messiness and sharp edges, but they definitely save me many many lines of code. There is always some weird thing that needs to be integrated/automated and shell is almost always the right tool for that.
If you can get away with using a single language that's good, and Python is probably the only one where that is possible (i.e. can write both prototype and production code, and data ingestion and machine learning). But I often have to use C++ because of the data size, and I think R's plotting is more convenient than anything in Python now.
The shell scripts have their messiness and sharp edges, but they definitely save me many many lines of code. There is always some weird thing that needs to be integrated/automated and shell is almost always the right tool for that.