Make it point-based. Allow for customizable squads, and each upgrade costs a certain amount of points. That way, people can create their squads beforehand rather than base-building within the game. As much as I loved the skirmish elements in DoW (capturing various points created a nice sense of urgency), base-building just seemed like an exercise in memorization and tediousness, just about like any other RTS. If they replace that with pre-game customization, all the better.
AoE3's concept of a 'RPG character' base was good. Your base would keep some upgrades as you levelled it up. Alternatively, SupCom Forged Alliance's concept of prefab bases. Good stuff. Or so I hear.