My ideas are inspired by the "super-weapon-level" commander upgrades. I think that there could be multiple suggestions, so I think it is a good place to start with something big, and break things down from there, adding polish.
So far, here is my understanding of the commander superweapons:
Guardian: An unbreakable fort, rivaling desolators, with the advantage of being both mobile and (potentially) a powerful builder, depending on the tech
Recon: A hit and run commander, capable of being anywhere where attention is needed
Engineer: Grand support
Strike: An empty vessel
I Guardian: Stone Statue Upgrade
Makes the guardian's speed limited to 10 elmo. It can still be lifted by hercules.
Overall, this upgrade says, "The guardian isn't moving anywhere, and he WILL take down the enemy if he has to!" He is still vulnerable to all the anti-heavy weapons (maybe, with exceptions, during the "stone statue mode," which makes it nigh-invulnerable at the cost of having to "deploy" to move around. Going into the theme of an "ancient protector, born anew")
II Guardian: Orbital Bombardment
Makes the guardian's range ridiculous, similar to a bertha, with the ability to relocate.
This is an experimental idea, but it should be fun, as such a weapon can only be built once. (Since it is similar to the stone statue upgrade, there is potential to give the stone statue upgrade... more mobile utility, with the commander being able to relocate few steps at a time with no speed penalty. This feature is up to debate.)
I Recon: Infiltration
Makes the recon able to teleport to ANY point of the map. Replaces jump pack.
The goal of this upgrade is to say, "If your commander can take out something, he will take it out. This will sacrifice the commander."
II Recon: Jetpack (bad name)
Makes the recon able to fly. Replaces jump jet with the ability to switch from air to land and from land to air.
The goal of this upgrade is similar, except this leans into more of a support role, taking empty spots swiftly. Can synergize well with nanolite upgrades, or any other.
I Engineer: Ambush (bad name)
Upgrades the engineer's cloaking field to give phantom's cloak, increasing energy upkeep for the ability for the units to not be revealed when firing. (Can have some issues with rapid-fire units)
This turns the Engineer into a top priority target for the enemy to take out, for the nice bonus of one of the greatest cloaks.
II Engineer: Maintenance (bad name)
Upgrades the engineer to sacrifice his building options for a powerful repair beam, similar to Future Wars rejuvinator
The Future Wars' rejuvinator is a hella cool idea, and it seems to be very in-theme of turning an engineer into a mega support. Maybe it can help heal striders, with potential negatives when the target gets hit or smaller units or other ideas, too many to mention
I Strike: Resurrection
Allows the strike commander to resurrect its wreck, similar to the undead, after dying. Does not work if its wreck is teared to shreds.
Placeholder idea
II Strike: Detonation
Allows the strike commander to make a big explosion, similar to the self-destruct option from Future Wars
Placeholder idea
OPTIONAL:
I ANY COMM: Advanced tech
Lets the commander have unlimited amounts of upgrades.
II ANY COMM: Cheap tech
Allows the commander's remaining upgrades to be ridiculously cheap. The limit remains. Cannot be used with Advanced tech upgrade.
These ideas are up to debate. (I claim no credit, as I have learned the hard way)