Taken from the Context of NS1
Preface: I understand that Commander Mode will most likely be different from how it was in NS1, and hopefully made easier. Here are my ideas to not only make it easy to learn, but easier to play.
First off, lets put down some ground rules: NS1 was based around generally a 6v6 team format, with a maximum of 8v8 for consistent balance. I'll assume this structure has remained unchanged.
1: Soldier Selection
Bounding boxes are good: We know this. But furthermore, soldier selection shouldn't have to be exact. Allow plenty of room for error, that gets smaller as they get closer to other players. Don't get ridiculous, but if someone is 20 pixels off on a single click and its the only marine around, we can assume they were wanting to select that Marine.
As to selection boxes, this is always a hard problem to fix, but there is a potential solution: Why not have an alternative to the box(or shift clicking to add selections) that eases selection: Selection Painting. Stole this idea from what is apparently supposed to be in some 360 RTS, but the idea would help with the unpredictable nature of Marines- if the selection goes over a marine when they are there at all, they're selected. It wouldn't be used for exact things, but its faster than a binding box.
2: Weapons & Upgrade Systems
The old system of "Drop Weapon" was nice, but you couldn't really ensure a certain player was getting it. Instead of that, lets make a few distinctions: Allow it so you can select a marine, and in the menu all the available weapons show up, and clicking one "buys" it for that marine. Upon going to the armory, the marine can select to take it.
Furthermore, the armory should be able to have "stockpiles" of weapons. Why not 'buy' 5 shotties for your team, and they're all in the armory- upon going to it, you just use it, hit 1, and tahdah, you get the shotty thats in there. This also ensures that you don't get people always asking for a shotgun, forcing the comm to take his mind off of what he's doing.
3. Then, Default Loadouts. Certain Marines are obviously your go-to guys. Why not have a selection to have a Marine get a default loadout that he gets whenever he hits the armory- Shotty, JP, etc. This way, your anti-resource guy always has his shotgun & JP so he can always be goin' round gettin' dem rezzezorzez!
3: Soldier Status Window
This would be a window, rather small, on one side of the screen. In this window would be the names of all the soldiers, with health bars behind the names, and on the right, a Checkbox for if you want to enable their default loadout or not(for those times when its time for everyone to go hive-hunting). Furthermore, this area would be easily seperated by squads, automatically re-arranging itself to Squad Numbers(SQUAD FIVE!). Furthermore, when your mouse is over this window, Units in the 3d space get their names overhead, so you could use this as a selection tool as well. Any orders that work in the 3d space would work here too- ordering someone to weld someone, for example. You could even have buttons to Med/Ammo/Catpack someone from here.
4: Custom Minimap Icons & Larger Minimap
I could see the minimap taking up much more space than before- 1/9th the screen even- and having it be useful. Furthermore, perhaps it is time we take in Supreme Commander's zoom idea: Why not allow zooming out to issue orders from the main field from anywhere? And mousing over a specific spot and using the zoom in would zoom to that position? This could potentially even do away with the minimap altogether.
Also, Minimap/Realmap icons are a must. And not blurry, badly-colored icons. We need color-distinctive, specifically shaped icons: Silhouettes of each thing. Soldiers should still be dots(perhaps Dots with numbers/colors to represent squads?), but have Phase Gates be an overhead silhouette, Comm Chairs be a side-silhouette, Armories being overhead, etc etc. For places where there are a lot of things, simply put a Miscellaneous icon- perhaps an Exclamation Point(!), that upon click would reveal whatever else was there(and allow you to select it).
5: Resource Tree
I don't mean the actual tree, as that is rather straightforward. But why not have a small UI Tree that shows the levels for Weapons/Armor upgrades, Weapons Research, and Tech Research? It could be as simple as 1/2/3 for the weapons/armor, and then Icons with grayed out/lit up HMG or GL, or Jet or Heavy. This could allow remote upgrading easily, and never let it get forgotten to easily.
6: The entire Commander UI. It would need to be redone, but frankly, the entire ingame UI of NS needs to be redone(which I plan on doing Mockups, one day in the far flung future). A starcraft-inspired bar at the bottom would mostly need to be gotten rid of(or at least made much smaller), and it would need an area dedicated to hints/soldier information.
Outside of these things, most of the problems would be relegated to Comms strategizing, and preparing, where they should go. Its better for the comm to have nothing to do but order people around than for him to be too overwhelmed to lead- at least one allows *anyone* to lead.
Also, I would reccomend a constant-tutorial system for the comm. Tooltips should have quick, concise, and most importantly complete
information, and be consistent. The "Build Armory" button should have a nearly identical tooltip to the "Armory" icon, except it would include Resource Cost.