Fancy/pretty or concise and informative plots?
I prefer plots which communicate information and tell the story so clearly, that I do not stop to think which software was used to create them. There are several good ways of achieving it and many ugly ways of failing it. The art of preparing a good plot (and infographics in general) is a complex matter and can not be boiled down to a one-bit answer like "do/don't use ggplot". 

To learn this art, read more papers, highlight plots you like and analyze what you like about them and how it was achieved. Try reproducing a nice plot in your favourite software. Consult your supervisor and colleagues for more hints.