Maybe the Leader unit belong in the Facility class, among with IC, Ports and Airbases ? Maybe even add a Fortress unit that soaks hits to make the list complete ?
Of course the Leader unit will be mobile, even if representing the command structure of a country.
His abilities would probably be better control and command of the other units. Maybe better Combined Arms modifiers between land, air and naval units ? Or a possible Joint Strike ability to add allied units in attack when they start from his space.
An Airbase can scramble fighters into adjacent seazones being attacked. Maybe a Leader can scramble fighters into adjacent territory when attacked ? Or let fighters land in a newly captured territory if the Leader is there too ?
If the Leader act as an Admiral, maybe let Shore bombardment boost up any matching infantry, like the Arty does ?
Or let the Leader implement some of the new rules from A&A 1914, like Artillery get a preemptive shot at landing units, and Tanks absorb one hit when attacking etc. I would even let a Leader combat move Tanks and Mechs through a newly captured territory to do combat in the second territory, to represent Breakthrough. Or let Tanks non combat move out of a newly captured territory, so they are not stuck there, this would be a supreme Strafing tactic.
Maybe even let a defending Leader retreat after first round of combat when being attacked ?