How did you make the leap from, 'there should be some, ilmited stacking' to 'Stacks of Doom are terrible and have no strategy'!
How about allowing for the creation of convoys, where you basically attach several units in a line for non-combat movement across an ocean or continent? Or if nothing else, change the system so it doesn't always default to the unit in the rear of a grouping to move first.

Another option for non-combat movement would be to allow stacking of land combat units when on a road (2 units) or railroad (3), with the condition that they only be allowed a relatively low defense value & cannot attack as a stack. Again, makes it easier for the player to move an army across their own lands while also giving an added boost to road- and railroad-building.