I realise it is very early in the development phase of AotS however the engine is clearly in phenomenal shape.

I would be surprised if the developers / community have not suggested any of the below, but as feedback is encouraged here are my two pence:

• Strategic zoom - Happy to not have strategic icons, I turned them off in Supreme Commander, but the zoom model here worked where you could go right the way out. As this game is naturally a similar scale, this would work very well here also, right now you can't quite zoom out far enough;
• Specify a patrol route - If this is there already ignore me but I could not find a way to specify a patrol route again much in the same way that Supreme Commander did it. I want to be able to specify a route and have the units patrol that route;
• Unit Aggression - The ability to decide whether the unit in question follows the enemy upon engagement. I suspect AI will not do this but I know that players certainly will. If you are patrolling an area of the map with planes a clever player will send over one plane to aggro your patrolling craft and then fly straight back over his base or defence area with a lot of AA waiting for them. It would be good if we could set our units to not follow to protect against this;
• Shields - Not sure if these are planned, but various levels of these would be good;
• Extend unit capability - This would need some balancing but the ability to add an AA gun or something similar to an existing unit that did not have that capability;
• Cyber - Some form of hacker to steal intel or unit blueprints from your opponent to allow you to build them;
• Super weapons - I've already seen the plasma storm (it doesn't seem to do very much damage). I thought at first this would be like the lightening strike in C&C RA 3 I think it was which was pretty devastating. I think something truly devastating would be brilliant, especially with the graphics capabilities of this game. Imagine a nuke or some Orbital base crushing event. However, as with Supreme Commander you should be able to come back from this with the right strategy and tactics. There was nothing better in Supreme Commander than fighting back from nearly being wiped out to then being victorious, especially in a 2v2 when the opponent left you alone and slowly you built back up and fought back. I think if Shields come in then something like this would be needed, also they can be turned against their opponent, remember the paragon in Supreme Commander? If you built that in your base and it was destroyed half of your base went with it, so there was a good balance between reward (potentially game ending in your favour) and risk (potentially game ending against you);
• Special Ops - Some unit that can scale the terrain would be a useful strategic tool at your disposal. Some special operations type unit that could scale up the cliff to a base or defence area and plant bombs to damage / destroy units and buildings. This would force greater use of radar and intelligence to protect key areas of the map;
• "Experimentals" - Loved these from Supreme Commander, they cost a lot to build but some of the battles that ensued with these in play were truly epic;
• Naval - Brad has said this is coming in an expansion;
• Transports - As the maps are so large you want to be able to transport units across the map. Supreme Commander had both teleportation and transporting aircraft. I preferred the transporting aircraft as they were vulnerable (balance) and you could spot them on the radar, if you saw a chain of greyed out squares (because you hadn't sent a unit over the top of them) on the mini-map, you knew that your opponent was transporting units across the map. Teleportation of the SCU's was often exploited to get them in the back of your base and start taking out your eco so would be against this;
• Defences - This might be a little hard to do, but C&C had the obelisk / tesla coils as base defences these were quite powerful. I know we've got the missile battery thing in AotS but something else like an obelisk, tesla coil would be awesome;
• Destructible map - Remember C&C and CoH where a bridge could be destroyed and you could create a choke point. Engineers could also repair the bridge and balance that out. Now I know you're sitting there saying "but the units can hover". I know, and my request here would be for something similar to the above scenario that fits into the game lore. Equally Supreme Commander did a good job of using terrain deformation which units could use to their advantage e.g. a crater could hide some tanks in which could use the crater as cover and hide down behind it.