Would be great of the transwarp cooldown would count when you are offline.......

It struck me as odd, too, that it's cooldown is ingame only.

If you've logged off for half an hour, how is that any less "not using it too often" than playing for half an hour?

Not only that, but it seems to only proceed with the cooldown counter when your ship is in space. The cooldown counter stops whenever you're controlling your character on the ground.