Different explosions!
Could be a couple different things, including explosions recolored to other specific colors (1 unlock per color) or being able to choose which color(s) your commander explodes as (1 unlock, possibly customized with RGB values; also can be changed after unlock). It would be noticeable and look good.
Chicken chasis!
Identical to the support (or pick a different one) commander, except it uses a chicken model. The idea is from the (weaponless) chicken commander that was used to replace people's custom commanders as a punishment, but isn't anymore, since people were deliberately trying to get it. Let them have it! (This one seems the easiest to implement, since something similar has been done before)
Different dgun texture/sound!
Retexture/add a new sound for the dgun blast. Make it a different color, make it look different and more dangerous, or make it sound like metal being torn apart.
Extra animations!
New animations, like an idle action or something they do when they are self-destructing.
New speech bubbles!
Commanders would say things like "I can fly!" when they are going fast enough through the air or after a long enough time that way. They might have a speech bubble like "Good-bye" when a nuke is a few seconds away from hitting within a certain distance, or say "SHINY" if they survive a nearby large explosion (singu/moho/detri/nuke).
I doubt all of these ideas can be done, but hopefully some can.