Hey everyone!
There is at least one important item that didn't make it into the post: In 1.2
AvA missions will now provide credit income. It's the first step towards making AvA a little more credit neutral, and not requiring AvA players to grind other game modes in order to compete. Please note that this was implemented with a slightly different system than how credits are given in match-made, to prevent some farming exploits.
Territory Upkeep is in place to discourage groups from growing excessively large, and to encourage top groups to fight selectively for what matters most to them, or hurts their enemies the worst. If the upkeep is hurting your Agency, you should consider reducing your size to something more manageable, and something you are able to sustain for a longer period of time. You could always use the territory trade option to setup some deals with other Alliances. Per my previous comment, the issue we are working on fixing with the upkeep is that it requires your players to put in substantial time outside of AvA in order to compete. If all your group wants to do is AvA each night, we want you to be able to do that. We may have some more substantial changes to upkeep in the near future, as we make AvA stand more on it's own, but the premise of an "upkeep" on territory as a growth limiter will remain the same.
For Blue: When adding up the total number of territories you control in a zone, any territory not connected to your Agency HQ is just counted twice. So owning 4 connected territories and 1 un-connected means you have "6" for upkeep purposes.
For smaller territory owners it won't hurt them hardly at all owning a spot or two away from their HQ, because the total number of hexes they have is low. So, you are not stuck just fighting the territory around you, but you are encouraged to not have a
large number of satellite territory holdings, especially in areas that are not of value. This is also why we are adding in theft missions now; when you reach a size that is easy to sustain and defend, start running theft missions to supplement your production and limit that of your enemies.
As an aside, we're fairly sure most of the large Alliances holders can distribute territory amongst their agencies (assuming they trust them) such that they incur only a minimal tax increase. This does mean individual Agencies within an alliance will tend to cluster their holdings together more, but that is also a behavior we wanted to encourage.
Bidding: We'll watch the results of the bidding change to personal funds closely, and adjust as needed.
This change does not preclude us adding additional features in future patches. Our goal with this change is to make it easier for more players to participate in AvA, and this does make it so
anyone in an Agency of 10 players can lead a strikeforce, while also providing some short term financial security for large groups that need more strikeforce leaders.
On the 50% player tax limit: You can still run things "your way", assuming you can convince your players to donate the money. We're doing this because total tax control has created numerous issues with players burning out and leaving groups, which overall has a
negative impact on participation. Additionally, many Agencies have not used the funds from high tax rates to get their players into the upgrades they need, which in turn is creating a substantial disparity in the quality of teams fighting, and
again reducing the quality of AvA overall. The "if you don't like it leave" tax rate mentality does not have an overall positive effect on the game, but choosing to donate does.
Our stats show that No-Facility maps are played a lot more than you might think... it's hard to tell as we currently load in the Mine map for it.
Peebojam, if the requirement of having at least 10 members in an Agency seems like it is hurting the smaller AvA participants, we'll look at reducing the number. Our current information leads us to believe this will not be an issue. Keep in mind, most games don't even allow you to
form a player group without a set number of players.

As a practical matter, Agencies with fewer than 10 players are not going to make strong territory owners. They can, of course, participate in other strike forces, they just cannot lead their own. But again, we'll keep an eye on it.
Blue, you can indeed select which territories a defensive facility shields. You can change the configuration at any time (in the Facility management panel), though there is a short delay before the shield comes up each time you make a change. (<10min). You can shield allied territories, or your own. Defensive facilities themselves can never be shielded, however. The higher tech defensive buildings are currently un-available, and will come with additional features of the lattice system in future patches. We thought it was important to get out the Tech 1 building sooner, along with theft missions, for many reasons.
Shayl, Theft Missions can be done on Mines, Factories, Labs, and defensive facilitates (to shut them down). You get more reward for higher tech buildings, and more reward if they happen to be on bonus resources, but any facility of those facilities are valid targets. Actually, I'd be surprised if Factories were not the most popular, as you get completed items out of those (though granted, resources from mines can be accumulated to build something better). It's also worth pointing out there is a rare change of getting something very good out of a facility during a theft mission. Raiding a Tech II Factory may get you commonly tech II hubs, tech II beacons, or a set of android squads... but occasionally it might also pop out a full mini-nuke.