I think with helicopters it's less an issue of control and more the optics - in real operations, you'll very rarely see helicopters just bobbing around in a hover over a single point, as that tends to be neither safe nor efficient. So, if anything, I think it'd be the opposite of full command - instead it'd be good for helicopters to have a little more autonomy in terms of being able to move around and away from battle points, and decide to orbit, change altitude, or seek terrain cover on their own. But I realize that's not such a simple thing to program!
As for resupply, I'd love to first see it in campaigns as a between-mission feature. Since weapons and ammunition are individual DB entities, I think it should be possible to do some basic calculations based on total number/point value of units using each type of ammunition, and their max loadouts. Then the player would simply have to "spend" a certain number of replenishment points after each campaign battle to stock up ammo (and potentially customize loadouts) - with less common ammo types (as per unit's max load) "costing" proportionally more. It could be just a one-stop "refill" as the current replenishment works in campaign, but optionally it'd certainly be neat to be able to fine-tune loadouts, take only what you need, or "scavenge" leftover ammo from weaker units using the same round types.
One thing I'd like to see is a more detailed damage and casualty system that could also work the same way (I.e. having to decide whether to spend points sending vehicles to repair, or casualties for evacuation, or bringing in fresh replacements. Doesn't have to be anything too detailed - but it could make for some interesting decisions, e.g. deciding whether to invest points into recovering damaged/wrecked units that you will not be able to use until one or more battles later - or getting a more expensive replacement NOW, but bringing it in with a training penalty and/or potentially denting your force's morale if you don't prioritize taking care of your casualties and abandon vehicles that could've been recoverable.
I think it'd be neat to see - and between campaign missions would be a pretty good place to try it out, since it doesn't really require doing anything "live" on the battlefield itself.