Ggplot is extremely powerful if you can grok its grammar, which takes some getting used to. But I'd assume that if you see a graph in a scientific paper it's made with ggplot.
Having many data points you want to explore you are always going to be at the edges of what your hardware and software can produce.
The last really big datasets I worked with were for my thesis and I had to do subsampling to below 10% to get results within 10minutes or so and that was basically plotting midi recordings of piano performances, so nothing gigantic
