To add on the the planet colonization, maybe some planets will have some native population which inhabits the planet. Players have to negotiate with them first. If it fails, they will have to take the planet by force. This way, it does not give planets free planet. They have to go through some hardship to colonize it by battling against the ai defenses. At the end of the war, the player can choose to kill off the residents or win their support and allow them to be part of the population of a new government which can enhance the rate in which the city is rebuilt instead of getting your residents to come over from another planet.
I like this. It adds a nice political side to this. I don't like the idea of taking the planet from natives by force, and don't really want my game to express that as something of value. Or perhaps if you do, you will have a constant hindrance of locals sabotaging buildings and laying mines etc... i like that you need to negotiate first to claim some areas. perhaps area's more rich with resources. However, this mechanic would require considerable thought and work in areas unrelated to the targeted fun of the game. I think its good, but probably not in a first version. The genocide portion though I would immediately choose not to use.
Maybe you could provide more support for the non-battle aspect by creating a market where you can sell weapons you have built or maybe loans where player can borrow troops from other economic player for a fee. Also, they can help to guild manage the new cities which have been colonized, by managing the construction of buildings and defenses as well as how the economy of the city will be structured.
I like this idea. Perhaps squads don't need to be military only. Perhaps they can be road builders, or construction crews with the knowledge to build certain things. Then, they can be sent into the hot zone as well, but with non-combat objectives. But also towards construction in general. Perhaps Guilds have schools that your construction crew can attend to get better/faster/more effective. Perhaps towns with more resources than squads of builders can also hire out other squads to build things for them. Costs slightly more in the long run, than training your own, but sometimes you don't need the long run, perhaps money is easier, like in the war zone where you need a lot of things fast.
So you mean something like allowing your guild mates to control your troops while he is offline? Maybe it could work this way. Before going offline, players can set one of their guild mates to command their troops so that they will not lack of man power should the player gets attacked. It also can help to resolve the problems of the timezone, Asian players may be asleep while American players are very active.
I liked the direction of multiple players controlling offline regions temporarily, and have opened another thread to address it, which has had some feed back so far. I like your idea of assigning a specific team mate to take over, and I've been considering approaches for other players not even known, to take over and assist. As well as AI. But I want to address one specific thing here:
Asian players may be asleep while American players are very active.
I like this idea of building teams based on people you never meet. for instance, establishing a time range that you are typically online, if in an active battle. And establishing a chat/forum/pen pal system for people with other time slots. The idea being that you have other people who can take over, with similar skill sets. Be kind a good way to meet people all over the world, and learn about each other in real life, not just limited to your time zones.