I thought about doing a series of these, but I probably won't, so I'll just list some of the other things I'd like to see, which overlaps with what you're talking about.
Air... air units should have a much shorter range than in FA, and require a lot of infrastructure to operate far away. I think this was probably part of the original vision for Supcom since we got the refueling station thing, but it was never used. Air should be more powerful than it is now, more expensive, but also require a lot more infrastructure with close by fueling depots. The exception to this should be bombers.
That would give units like aircraft carriers and land based air carriers a real purpose.
Transports should carry many more units and be much harder to kill. In exchange for this, they should have a massive radar signature and higher cost. Alternatively there should be T3 and T4 air transports for each faction.
One of the things I hate the most about FA is the air balance mechanic. It should be some kind of paper-rock-scissors style mechanic, instead you just build T3 interceptors until the end of time. The entire category of air units is dominated by that one unit, which cannot be countered by other air. That leads to mass hording of T3 interceptors in games and battles of attrition which is just boring. Interceptors should have a counter, and air should be re-worked to require multiple types of air units for both attacking and defense.
A simple way to do this would be giving transports EMP that disables interceptors but not gunships.
Transports > Intys > Gunships > Transports.
Obviously if this were dropped into the game as is it wouldn't work, but if you started with this kind of system and built things out from the ground up you'd get a better system for air combat.
Yeah, generally supply lines would be super useful, supply lines and support vehicles.
The quantum gateways were probably originally designed to be logistics units. You were probably supposed to build two and link them, and then you could teleport units around the map. I think that would make a lot of sense, and enable play on really large maps.
On the naval side, I imagine they originally intended for Naval to be closer to real life scale in Supcom, but backed off on it. Naval should have been something reserved for only the largest maps, and it probably should have revolved around amphibious assaults. You build naval to ferry land units and not for its own sake. It would have made some of the larger maps viable. Generally Supcom lacks sufficient transport mechanisms to make the larger maps enjoyable. Spinning up on those maps takes too long, and reacting to new information also takes a really long time. Higher capacity air transports, massive capacity naval transport, and late game teleporting gateways would solve those problems and make games on much larger maps more enjoyable.