I think the strongest use case for interfacing R with JS (be it through plot.ly, Shiny, rCharts etc) is when there is more serious statistical modelling going on (i.e. plotting things like credible intervals or model coefficients). But often you find that you add a 'statistical layer' after you already have an existing plot (i.e. adding a confidence band to a line plot). Maybe it makes sense to have one tool that handles all these cases.