I would just like to make one simple suggestion: Usually when you order a commander he will move to where you clicked and bring his whole swarm with him. Sometimes he's even the first unit there, which almost certainly kills him
How about we make it sort of a reversed sensor vehicle? Instead of artillery following a sensor vehicle around, people would order their comm to move assigned units to where we clicked. The commander should use some algorithm to pick the most "central" unit in the group and follow it around. Logicaly, lone commanders would work like regular units.
There, commanders aren't as fragile any more
Another idea: Unify sensor and commander assignments. If you have an attached sensor unit and press shift (for example, any other key would work) while left-clicking an enemy unit, that sensor unit will move up and target the enemy. Likewise, artillery units in your swarm would automatically make use of these spotters. Should the spotter die, a commander would also automatically request one (maybe make this a check-mark on his options and also a check-mark on the design screen for designating the spotter a commander would order from a factory). The idea is making this work with dynamic factory reinforcements someone suggested.
This has many advantages: It makes commanders feel more like they're making your job easier and therefore immerses you more in the game, and makes mobile artillery units not run the risk of becoming "orphans" without their designated spotter.
We should also change sensor assignments so it doesn't work based on a fixed "safe" distance. Assigned units should keep further back according to their firing range.
Other minor suggestions:
Shift could be use for artillery strikes on a target, Ctrl could be used to direct VTOL strikes (again, using a dedicated VTOL strike vehicle) Shift and/or control dragging would designate an area for strikes. Holding both keys would make a combined artillery and air attack. Spotters are independent of other group orders while carrying out these missions.
You hold Control and Shift to drag a rectangle around small outpost for bombardment and VTOL attacks. You left click in the middle of the outpost afterwards. Your direct combat units swarm the outpost while your artillery and spotters keep bombarding the areas your marked until there are no more targets or you hit a special "Abort all operations" button.
All of these are rather simple to implement compared to all your awesome ideas, but would make commanders useful that much quicker. Perhaps not enough, but it could be a start.
In another note, just to add to someone else's article:
Has anyone ever played the first Perimeter? The AI is absolutely amazing and as soon as it's completely turned on (you'll notice when you see it) it will start kicking your ass. It would attack your least defended positions, it would use the most effective units it could, it would deploy artillery to support itself, it would surround you... The only way you could win was to "cheat" by capturing parts of it's base. In fact, a main part of perimeter was disabling parts of the enemy base and capturing (think power-lines and taking them out to replace them with your own). That sort of AI is no fun in a conventional RTS because you know you will never outwit it. Perimeter was fun because it gave you a way to outsmart it in another area.