Alliances is interesting. It would be cool if you could pick a set amount of players from your alliances and much like picking a team for GST send out invites that they would have to accept to participate.
Also I was thinking to be able to start a war you would need atleast 15 members in your guild. That way not every noob with 2.5k can start a war lagging up the server.
Was also thinking about the possibility of connecting opposing guilds, guild houses together when they're at war so guild houses can have some relevancy.