Not sure all of these belong in the same game:
Heightmap affects battle mechanics. eg: units on mountain means you should be able to shoot further. Driving up hill should be slow. Shooting whilst moving should be less accurate. All put together means 10 tanks sitting on a hill would mince 10 tanks coming to kill them. This would make unit movement tonnes more strategic and less about remembering or noticing something. It would make map control way more interesting too, would give you something to fight for besides mex: the highground.
Better unit movement physics eg: Land units can get airborne if driving too fast. They land and slide into each other which damages them, then crash into a factory which damages it. Different surfaces have different traction, affected by weather.
Dynamic units eg: UI allows you to set unit speed, so you can choose between careful speed and fast. Different options for shield (size/hp/powerCost). Different options for t3 arty (accuracy / reload time). Different options for overcharge (damage / reload time). Slick ui to set settings for one unit, for groups of units, for all units of a type, for similar but not same units.
Ability to delegate tasks to an AI assistant eg: "Use these tanks to kill that stuff", "Reclaim all that stuff using these engies", "spend 10% of my eco expanding my eco", "increase my air production until i'm using all of my power". "Scout for me". Hmm, maybe this could have been a nice feature for SCU's.
Engineers can raise/lower heightmap. Which would make fortifying your base more interesting. The GC can't even walk to your base anymore.
Flowing rivers that can be dammed, then the dam can be broken, creating an inland tsunami, destroying all tanks that aren't amphibious. You start by using your engies to build the concrete damn then mass up auroras. When you blow the dam it sends the water into their base, killing some of their units but also sweeping your own auroras quickly passed the point defense, into their base, where they start killing things.
Flowing lava that can be redirected by changing heightmap. Nuking the volcano to trigger it.
Avalanches where you can blow the cliff, crushing some units, blocking the path at the critical moment.
Customizable units where you can decide the design: what guns will it have? engine? etc. So you adjust the speed, dps, abilities and cost of the unit, then mass produce it. But first you have to upgrade your factories to be able to build it. If you find a wreck of a unit with a gun you don't know about it, you can capture it, research it, then use it. This is totally a different game now
Transports that work.