I don’t think plots should be on the homepage for the Julia programming language
I actually agree with this point. I only thought it could be appropriate because of the Gadfly selection of plots (I find it misleading to have only one of many alternatives appear so prominently in the homepage), but maybe the way to go is removing the display and instead add some charts of Julia related information (number of downloads, number of packages, stars on GitHub etc).
As for the topic of this thread, I’m also in the process of using Plots (with GR) to create publication quality figures and it is true that there have been some hiccups, but the best solution is probably reporting all the issues in detail and then maybe writing a blog post with a set of instructions (or even create a set of PLOTS_DEFAULTS that are appropriate for publication, if such a thing makes sense in a “cross-journal” way).