you should be able to modify the commander. i think you should be able to choose for your commander to be better in one way more than others. EX: you could make him more resourceful, so he gives more power and metal, or focus him on one of the 2, basically being able to upgrade the commander is what i mean. you could make him build faster, or make him more battle ready (more attack, or more defence, or both with a loss in build ability etc.) you could also make him more useful by making him able to travel planets on his own, but making him the only unit that doesn't require an upgrade to do so.
I see you're new to the forums, and welcome! You should do a search before posting, in accordance with the forum rules. This has been brought up a few times in the past week and is a common topic. Commander upgrades are a confirmed no. In short, the Commander is your general. He shouldn't be flung into the middle of the fray. He's not intended to be a late game combat unit. You should search around and check out some of the several discussion threads. Lots of opinions tossed back and forth.
i make it short ... upgrades confimed no ... balancing the commander in some way ... may be .... Still .. commanderrole is building stuff for it to fight ... not to fight itself .. If commander dead then all your stuff also dead then you lose Next time i may use ikea picture explanation ..
THe closes thing we'll get to what you're talking about is commander abilities. These are different pre-programed abilities that commanders will have and depending in the commander you select you will get what abilities he gets. These abilities aren't game changing though and I think the'll concern the commander only (it wont be an ability like all your factories produce 25% faster). They are a small bonus that the commander gets. there were non confirmed yet, but IIRC the'll be going along the lines of this commander produces 10% more resources, this one has self repair, this one fires hit uber cannon 5% faster, etc. EDIT: the only way to get and customize your commander with an abilities of your choosing was to pledge more than 1000 dollars when the kickstarter campaign was going.
You'll have to wait for mods to do this. When the game is released we'll have access to the server files and you can be sure that they'll be a couple commander upgrade mods and they'll likely be very popular.
Every Commander demands a central ability list to function against other Commanders. But pure everyday stat buffs are boring. Go for big changes to mostly unused things. Here's a few things that might be cool: Bonus points if you see what I did there.
They answer this question in the Planetary Vanguard Newsletter Issue 1 https://forums.uberent.com/threads/the-vanguard-newsletter-issue-1.54922/ Under "Commander Abilities"