I would also suggest unlocking those states, powers and abilities through mass killed values, like levels. Small scale stuff gets accessed early on, with few kills, higher level things get accessed after the ACU has seen a lot of combat and killed a lot of mass. And an "ultimate" ability, one that takes a lot of mass killed worth to gain access to (so you cannot have it too early), and can only be triggered either 1x in the whole course of the game (like for example summoning a powerful unit or erradicating whole sections of the map), or would take a long time to cooldown.
Doing this would bring much more value to active ACU usage, and not keeping it in base to eco or hide in the water. He who uses the acu more and kills more, levels up faster and gains advantages from it.
It would also make attacking your enemy when you have superiority a double-edged sword, because you know you have a big chance of feeding the enemy ACU when you do it.
Mind you, I think it should not go too much towards making the ACU itself an indestructable beast, because one of the many charms of SC is ACU sniping, and how sending your acu to the front lines or telemazoring can quickly and easily turn to your defeat with a quick snipe of your ACU. An acu should, in most cases, run away from experimentals and not become one :p Or if it does, then hp gain must go at expense of DPS.
Just my 2 cents on the matter
Check out my 2 maps: "Survival_Mayhem&BO_3d_v1" "Survival_Mayhem&BO_3d_RPG"
as well as my mod: "Survival Mayhem&BO balance"
-- let me know of any bugs or issues regarding those 3.