Frogboy, i have a few ideas about how to make it a war and not simply battles.
We may should have to concept of battalions. This would be a large group of units / meta units flagged as being a battalion with and objective we would assign to it. For example : Capture and hold a specific position on the map. That would mean we would have the option of letting this battalion managed by AI. In addition this battalion could request by itself for re-inforcements. We as commander, would be responsible for producing these re-enforcements. Ask for re-enforcements would come from all the battalions we have created and assigned an objective.
I get where you're going with this but I don't like it for the simple reason that you're giving up too much decision making. They player needs to actively manage each battle. With a battalion managed by AI, even partially, the game starts playing itself. The most I want in terms of auto-decision making is for a unit to attack another in range, engineers aiding units on their patrol route and so on.
While we're at it, here are a couple of ways we could improve on unit behavior. I'm going to assume that the mentioned units work more or less the way they do in FA. These thoughts all fall into the category of giving units a more "human" judgement (yes, technically we can call that AI)
Engineers: If patrolling, they will often aid in the upgrade/build of a structure. They need to stop if their aid is draining resources to a critical point. In FA they'll keep aiding the upgrade of an extractor even if their aid is taking resources well into the negative.
Unit retreat: Units need to have better judgement as to when retreat and repair (thinking air units here). So, if a gunship is under attack by 2 fighters and is taking slow damage but another 10 fighters are inbound (an air unit would be able to see it, it has its own radar with access to the base's radar) it would turn and run for repairs knowing that before it gets back to the base it'll likely be 3/4 dead.
Air units: Have the option for the unit to strictly follow its patrol route. Way too often air units will chase enemies that cross their path half way across the map, usually leading to their destruction as they pass over an enemy base and get taken out by AA. In a war, units need to follow orders, not take off and disappear. Yes, engage enemies approaching the base but don't chase them too far as they retreat.
Spying. I don't remember which one of the C&C games introduced it, but the idea of a stealth unit would be awesome. I still remember the Stealth Tank. Next to no armor and limited firepower but if you could get one into an enemy's base early on it would be a great advantage. Of course, it is discoverable by troops, so it's not completely immune to destruction.
Enough for now. All this is making me want to play FA. I also just upgraded to a 3440 x 1440 ultra widescreen and it just gives a whole new perspective to FA. 7 years old and it works perfectly with a resolution that didn't even exist back then. Now THAT'S a good engine!