First of all, zoom. In large and huge maps, it's impossible to get the full map onto your screen. It's much easier to manage your troops when you can see the big picture.
Secondly, alliances. If you click on a user's name in the sidebar that displays all the usernames, you'd be presented with many options. Request alliance, and others to be added later on (because I can't be the only one with an idea that'd require a user-specific menu). When you join an alliance, your colors are merged (based on the color of the person that initiated the request). The original requester keeps his color, and the person who accepted the request gets a different shade. From there, the leader (the original requester) can request alliances with others, etc. etc. etc.
Anything to add? Thoughts?