Darloth has created the mod which makes commanders much tougher.
I have made commanders much tougher.
Perhaps too tough, but hey, it's fun. You may need a gentlemans agreement not to wonder over and "inspect" your opponent's base though - commanders are now basically immune to tech 1 units except in vast hordes.
A detailed changelist is below:
MaxHP for all factions multiplied by 3
Regen rate for all factions multiplied by 3
Shield Upgrades doubled in effectiveness for Aeon and UEF.
Regen Upgrade slightly boosted for UEF
The cybran commander had no defensive upgrades save cloak and stealth - I couldn't work out a way of boosting the cybran upgrades without unbalancing things - I am open to suggestions! (PS: The cybran commander already has an insane self-repair rate now, at 45dps)
All HP and Regen buffs for veterancy have been doubled across the board.
All commanders have a short range, rapid fire missile defense system, which will discharge bolts of electricity from their fusion power supplies - these make them functionally immune to tactical missiles except in vast numbers. (I was considering adding a powercost to this, but by the time anyone has tacmissiles, you typically should have enough power, and a large drain seemed unreasonable. I could be persuaded to add one though if enough people want it)
Death Nuke damage has been increased to roughly 11,000dp - Commanders do not explode as often, and sacrificing one is a major loss. I felt their deaths should be more meaningful in that explody way.
Edit: Oops, and I forgot to say they also shoot at aircraft now, just like in the opening movie. However, they are very innacurate - gunships usually die, everything else probably will not.
In short, commanders now kick major ***, and after upgrades, are on the same sort of level as experimental units, which is where I believe they always should be. If you are using this mod, I suggest the Assassination gametype - rushing a commander is nearly impossible, and if you're not playing Assassination, there's no risk to using your commander as an early game experimental and shooting up your opponent's base with it, then exploding.
A nice upshot is that while the shield/repair upgrades can make your commander aazingly tough, he's now tough enough to make the other upgrades feasible choices without him being too vulnerable.
Aside from possible balance tweaks, I think I'm done with this. Any comments or suggestions are always appreciated though, and everyone is welcome to see how I did it, upload it places, and generally mess with it. The only thing I ask is that you credit me if you derive a mod from this or post it somewhere.