What if you add unit upgrades to its respective HQ? For exsample UEF land HQ could have an upgrade pressureproof shields, that would allow for Titans to walk underwater. Could spice up naval maps with it.
Or some upgrade that will allow idle transports to be able to build stuff like flying engies. Things along that line that give you more strategic options and flexibility with your units, so you can be creative how you play. They should be quite pricey if you want to invest in it, but same goes for your Commander upgrades.