Just thought up a rapid system for making custom armies that accounts for balance and prevents powergaming.
When creating an armies, you will have 5 points (Though this can be altered on skirmish matches). These points can be spent on the following.
Troops (Limit 3)
Vehicles (Limit 3)
Aircraft (Limit 3)
Powers (Limit 3)
Buiildings (Limit 3)
All start at 1
Troops Level 1 - Machine Gunners, Missile Troops and Engineers
Troops Level 2 - Can build a faction specific unit, plus minor upgrades
Troops Level 3 - All troops have bonus training when built, plus access to a hero
Vehicles Level 1 - AA/Missile Tank, Light Tank and Harvesters
Vehicles Level 2 - Can build faction specific units, plus access to minor upgrades
Vehicles Level 3 - All tanks have extra armour and firepower, plus access to a superheavy 'hero' tank
Aircraft Level 1 - Scouts (Unarmed drones that reveal map/explore fog of war). Can auto-explore.
Aircraft Level 2 - Light bombers and air to air planes. Minor upgrades
Aircraft Level 3 - Heavy bombers, training and more upgrades
Powers Level 1 - Access to low level powers like field repairs for tanks, scan area, or protect building from engineers.
Powers Level 2 - Faction powers like reinforcements, deploy stealth field, make a friendly unit explode on death.
Powers Level 3 - Can build nuclear weapons, ion cannons etc
Buildings Level 1 - Power plants, basic defences, vehicle yard, barracks and airport.
Buildings Level 2 - Advanced power plants, special defences like light obilisk of light and a faction specific building such as improved ore refinery. Able to build MCV at vehicle yard
Buildings Level 3 - Buildings get bonuses such as stealth for NOD, shields for GDI. Plus the ability to garrison units in the base buildings.
This system can be used to quickly make an army to your style. Just choose a faction and spend your 5 points.
I'd probably go for NOD, Troops 3, Vehicles 1, Aircraft 1, Powers 2 and Buildings 3.
None that I can think of. This limits the min/max problems with a fully customisable army.