Hmm. I think introducing this would make players want to do other things, as well - changing some admins at a colony, say, or managing their cargo, or something else of that nature.
The problem, generally, is that sometimes things happen where the game needs to show a dialog. For example, let's say your fleet loses its last ship due to lack of supplies and an accident, or a mod shows a dialog for some kind of event happening, or a tutorial info dialog needs to pop up, etc.
Then keeping the main UI open would prevent that other dialog from showing up, so it just gets weird trying to deal with this case - it *mostly* works (in fact, you can unpause the game while the map or the rest of the UI is open, in devMode), but where it doesn't work, it's a real pain. Not that it couldn't be worked around somehow, it's just a lot more effort/testing edge cases/etc than it might seem at first glance.
(For stuff like fleets, you could, say, force-pause the game is a hostile fleet is nearby/chasing the player, and that'd mostly take care of it. It's the other, less-well-defined stuff that's more troublesome.)
In any case, I've got some thoughts for cutting down on hyperspace travel time as the player gets deeper into the campaign, so that's another angle for addressing this
