Seems like a simple but powerful idea. Just allow us to invert the polarity of audio going into or out of a given channel on a plugin right at the pin connector. Right-click doesn't seem to do anything in that window, so it seems like a good candidate. Right-click in an empty box to fill it and invert. Right-click a filled box to toggle polarity.
A very crude mockup. I made the "-" red because I felt like white or the grey background color might not stand out quite enough, and I think it might be important to unambiguously know just from looking if one of the channels is inverted.
Bonus would be a pair of buttons (very crudely rendered in the following image) to quickly fill in the input side for M/S Encoding and/or the output side for Decode:
This shows what happens after you click both of those buttons. Each one would fill in its corresponding side appropriately, overriding whatever was already there. Maybe they could be toggles, but then it would need to remember where it was set to begin with. Of course, it's easy enough to just save presets with this already done, but the buttons would make a nice convenience as well as filling some of that negative space in the window.
Course then we'll have people realize that "M/S" mode for ReaEQ isn't what they hoped for since both channels get the same treatment, but this could be useful in plenty of scenarios, not all of which have anything to do with M/S at all.
Edit - And yes I understand that there aren't many cases where the configuration in my first picture actually makes sense. You'd probably invert at one end or the other and leave it, but...