The ability to keep in writing some information visible to both players --- say, "This port has already used 75% of its capacity this turn", or "Demolition unsuccessful", or other notes like that.
When preparing scenarios, for instance, you could have a stack with a note saying something like "These units can be set up from hex X to hex Y".
Ok. So we are looking for something like Post-it notes, aren't we?
What a great idea!
Now I have to figure out how it will fit in the "big picture", and how to plan it. It shouldn't be too difficult.
Another feature that may be useful: a button (or key, whatever) that when pressed hides all units, so that we can see the map beneath them without having to move stacks.
In version 1.2, during play you'll be able to switch ZunTzu to a special mode which purpose is to move board fragments and terrains around. In that mode, all counters will be hidden (or maybe very transparent, I have not decided yet).
Yet another feature: a counter in play still appears in a vague outline in a countersheet. This is useful, as we can readily see if a counter is in play; but it would be more useful if there was a means to locate the counter on the maps.