@Alan - I still very much think it was by design. Plot themes are just some sugar on top, not overly documented I think. For any plot theme, a set of options were decided on that someone like the look of.
So using a plot theme has the effect of overriding default values for any number of options, and I don't think they are documented explicitly what those options are.
It does mean that you can't use SetOptions[ListLinePlot, Plotmarkers -> None], because the `PlotTheme will override it.
You can still use the option PlotTheme -> None in your ListLinePlot and it overrides, but to make it permanent you have to hack it.
@halirutan That sounds kind of overkill. The Atom editor has an automatic GitHub issue creation feature. Maybe you can learn from them how to handle it optimally, as they should know best.
@Karsten7. It's not overkill considering the GitHub issue system is a joke compared to other bug-trackers. If I could adjust what users see per default, I would keep all issues at one place but spamming carefully handcrafted issues with several auto-created stack-traces doesn't sound like a good plan to me. Especially, when you cannot hide these issue.