Is there a sort of Turing completeness among plotting programs, i.e. can everything ultimately be done on any popular plotting program, or are there things achievable only in some and not others?
For strengths of plotnine, ggplot, and Altair over Gnuplot (or matplotlib), see section 3.3 of the article, particularly the example
ggplot(data=mpg) + geom_point(mapping=aes(x="displ", y="hwy", color="class"))
You can easily replace 'color' with 'shape', or even faceting (getting a separate plot for each class).
I do not know Gnuplot very well -- what's the easiest Guplot way to do this? [1] I do know that when I was looking at data sets, switching from plain matplotlib (where you'd have to plot in a loop over each class) to the grammar of graphics style was a breath of fresh air for me.
Separately, and less interestingly, if you are already using Python or Jupyter, Gnuplot isn't as smoothly integrated into that ecosystem.
[1]: The first thing I found on the website is http://gnuplot.sourceforge.net/demo_5.4/varcolor.html, but perhaps there's a better or more minimal example?