I think there just needs to be a way to set army groups. If I make six individual units an army I can always select them with one click on any unit in the army or from some sort of army management UI. They stay as an army until I disband the army, at which point they go back to being individually controlled units.
Armies should also be nameable, so we can have good fantasy names for each of our armies.
As for the other point, I think if they implement a way for you to upgrade size of a unit there needs to be some sort of penalty. The unit loses a level or two or suffers a temporary decrease in per unit combat effectiveness. There should be a real decision about whether or not you want to increase size of existing units. It should not be an automatic decision to increase everything once you learn the relevant tech.
Besides, you wouldn't add new people to an elite unit of soldiers and expect them to perform as well with the new people. Not right away anyway.