Commanders have never been treated all that specially in zero-k. Despite them being upgradable and feeling like a special unit, they're usually worse value for cost than something designed for the job.
They're one of the few units with a weapon and buildpower on the same chassis, and can do some things no other units can, but there's a vague design intention to make a superpowered commander an inefficient choice in most cases, so giving them special treatement would maybe go against that.
Point 1 - Stunning and other status effects are often aimed precisely at disabling heavy weight units, like commanders, heavy tanks, stuff like that. If you can no longer permanently stun a single heavy thing, how will the current system where stunning is a good counter to that sort of unit work? What should be changed to replace this?
Point 2 - I can see arguments both ways. I'd be fine with commanders not being capturable personally, though if they ever are it's because they're out of position. You can always destroy the capture rover to get the unit back, though, so I'd be fine with it remaining the way it is.
Point 3 - personally I agree, the various abduction strategies are a bit of a gimmick, don't usually seem to add that much, are -really- annoying to lose to, fairly easy to defend against if you know it's coming, and seem like just a holdover from TA or earlier games. I'd love to have any design intentions behind this explained to me though, if I'm missing some.
Point 4 - on the contrary, I love this feature, it's a natural extension of the ability to terraform. You already can't terraform out from under a building, but a mobile unit is fair game. It's often the only real defense many construction units have. While it needs a fair bit of micro, I appreciate that this is an area of considerable skill ceiling. It's limited in that it needs a builder unit (expensive and valuable, on the whole) very close to a source of danger. You can also counter it with your own builder units.
