In a perfect world, most of the ideas posted above would be pretty nice to have at your disposal. However, when you've got 5 squads with 1 or 2 people, maybe 2 full squads and a couple of others with 3-4, it's not quite that easy to say squad 2 do this or squad 5 do that. As a commander you have to use what's available. I wouldn't order a squad at the next flag over to attack a neighboring base IF a more cabaple squad exists. If Squad 2 has 2 people and is next door, I'll leave 'em there and order a full squad to move to attack or defend a flag. It's also very difficult when you KNOW a squad is available to defend a flag or arty or uav trailers or what have you and they flat out ignore you anyway. A commander's adaptability to every situation is very important to winning the round. Even more important is for the squads to be able to adapt to the commander's wishes. Ok, you may wish to go attack one flag 'cause, well, you can. But the commander can see a lot more of what's going on than the squad leaders. I'm sure the maps that come out will all be different, but there are a few things that need to happen:
1. Commander needs a squad for security and repair of radar/uav. Without these 2 items, a commander is basically useless.
2. There will be specific must-have's on each map; using oman as the only current example, the 2 flags to the west on the beach are extremely important to hold and defend at all cost. Any of the other 3 flags will be needed as well but those 2 are the most important. If MEC controls them, they can easily deny arty. If the marines hold 'em, they have a very powerful tool at their disposal.
3. squad leaders need to keep their squads in check and functioning to one purpose, not scattered all over the map. Due to spawn losses this is sometimes difficult, but still somewhat manageable.
I enjoy playing in the commander role and hope to continue doing so. It does suck quite a bit though if you have little or no support from your teams on the ground.