I'd suggest just using a good graphics program and using its defaults. This would normally look good enough, I imagine most journals would not be too fussy about such things. You probably also want to use a scripting language for reproducibility and efficiency. The following packages are reasonable choices, produce high quality graphics without much work, have reasonable defaults which can be tweaked if necessary, and export into the common image file formats like PDF, PNG etc.
ggplot2 in particular is designed to be very high level and flexible, and is based somewhat on the Grammar of Graphics book by Wilkinson, which describes a high level approach to data visualization. Specifically, high level implies ignoring the small details of your graphic and letting the program taking care of it for you.
The R package
ggplot2 already mentioned is quite popular. You could also try
PGF/TikZ and the plot package that uses it,
matplotlib is another possibility, though I have not used it much. Also note that both
TikZDevice though it does not seem to be actively developed. For
matplotlib, see matplotlib: Typesetting With XeLaTeX/LuaLaTeX.