Don't know if the pandora box of the input system will be opened again or not in the future (I suppose there are good albeit fun historical reasons why not:)). In case of the latter, was thinking to ask if it would be possible to give us some indication when orders aren't listened. It's not always clear when you're allowed to give orders already, especially during finishing or transition phase of actions.
Some options on top of my head:
a) I would prefer something like darkening / trasparency of UI elements - I think people detect the change in intensity even without direct look and yet it isn't overly diversionary.
b) On the other hand, pop-up icons or putting away the hud altogether might end up as too much disturbing, some actions are fairly short.
c) Have seen in adventures the mouse changing into turning wheels. That's neat. However, as multiplatform, I suspect due to Unity it won't work for all the systems, I'm not having the hand on linux.
If you would be open to something like that, then also making affected buttons non-interactive would make a sense.
Some mock-ups for illustration follow.
Darkening / transparency example:
As if closing up squares of AP indicator:
