Thanks to Kyrie for writing up the topic. There are, excellent, IMO, ideas in there. However, I don't think the highly organized nature of houses you are suggesting will work. I'll explain.
Correct me if I'm wrong, but MPBT only ran for a short time and never made it out of beta? If so I'm not sure if the command system was ever "stress tested" under large player interaction. I didn't play it so I don't know. What I do know is that I have played a game that has all out combat on a massive scale, with player run territories totally controlled by players, with owned territory and assets, with resources that are fought over - that's eve online. I'm a very long time player of that game and this is why I don't think some of your ideas will work, because I've seen how people in a game with a large server population interact with each other on a full time basis. It's just way more chaotic than you think it is IMO.
What I'll do is explain eve online's system of player organization for territorial combat - which is nearly no organization officially. At the basic level you have a corporation. This is very analgous to a unit in mech games - group of people who form together. It will have a leader (CEO), a XO (deputy or head director, depends on the corp) and officers (directors/assistant directors) who perform various functions assigned by the corporate leadership (recruiting, internal security, production management, facility managment for bases, etc). A corporation is an in game supported function - it is created in game, and players then join it for membership in game and become officially recognized members. However, that's where the in game control basically ends, other than the tools provided by the devs to support the functioning of the corporation (funds auditing, member management etc). The leader of the corporation is basically chosen by the members. This is important to remember because no one will follow someone they don't trust or consider competent for any period of time - if a corp is run by an ineffective leader, it will bleed members until it collapses or the leadership changes.
Remember this is a game and people can instantly choose who they wish to hang out with in their spare time. If the situation is not to their liking, they will leave - and this can happen quickly. The officers and deputies are sometimes also elected but in many cases are appointed by the leader (CEO) of the corporation. Corporation sizes vary but they can run from the 20's to over 500 - but larger corporations generally have an advantage in the territorial warfare department (can take more losses, more resource/financially secure, etc).
Now again, a corp is like a unit - just like you see people with unit sigs on this forum you'll see people with their corp sigs on a eve forum. It of course is not a house, or even a military prefecture (stealing the term you've used from TT). This requires corporations to associate together, in something called an alliance. An alliance is a in game supported function that basically ties multiple corporations together to in effect, form a super corporation. Where a corp has individual players as members, an alliance has full corporations as members. This then forms what would be analgous to a military prefecture or house. It will have a leadership structure; an alliance leader, a deputy leader, a diplomatic staff, and other officers to perform whatever functions are decided as necessary. The leader is generally selected by agreement by the CEO's of the member corporations and serves as long as he/she cares to and/or shows that they are good at it. If they aren't, the member corporations players will begin to complain to their CEO's and there will be a change in leadership or the corporation will leave the alliance. I've already said this once but
remember this is a game and people can instantly choose who they wish to hang out with in their spare time. Bad leadership is probably the primary way alliances fail, and you'd be suprised how fast that can happen.
The reason I've stated the above is this is why I think the setup you're suggesting with large formalized organization just won't work. If you end up under someone you don't like or respect, you can simply change the orginization you're with using a few mouse clicks. Having it organically form under player driven direction is much better and more effective to boot, as the people that are considered for these positions are almost always well known, respected, and competent - they are people that other people in game will follow. To put it in another way - you don't even NEED to have devs/game people to pick who goes where. People in game will do it themselves and do a better job of it too boot.
Now for territorial warfare itself, based on my experiences, you don't need hexes just have planets and areas of responsibility. This is how it's generally done in eve; corporations and groups of corporations are assigned to be in certian areas and cover them (in eve they "live" there and operate all of their operations from these areas). If assaulted they fight the initial wave while alliance leadership forms a relief effort/sends reserves to the area (other corps move in to help). It's probably going to be very different because in eve everything is very mobile, so to use a battletech example, a unit stationed on the davion front can be moved to fight the FRR literally tomarrow or even the same day (this is probably not a great idea in this game). The keys to making large scale warfare work are that you need to have planets with resources that are very valuable, and therefore worth fighting over. In other words, having them or denying them to your enemies
makes a difference. This will naturally generate combat as plans are made to protect them/take them, other less valuable planets are selected as targets for bases to make the attack/staging areas - all the good stuff we want. In eve fights of this nature can become very large as everyone and his dog jumps in on one side or another - I've been in a 1600+ man engagement for example, which shows just how much effort can be placed in them. Again, if it's worth it, people will fight over it, and fun will be had.
Now obviously MWO isn't eve, and shouldn't be the same. But I would urge everyone to keep in mind 2 key concepts that I think should be. With in game organization, less is more with regards to how much the devs or game should dictate. Let the players decide how they want to do things for themselves. What is right for one group can be really wrong for another group, after all. Second, place things out in the game that are valuable and worth fighting over. They will rapidly become centers of conflct and will drive the story in of itself of MWO with no effort or intervention from the PGI staff. I suppose this actually brings up a final overarching concept that I wish to bring up last - let the players control the community warfare game - trust me it's more fun that way