Change 1: Here's my number, zerg me baby.
Resource extractors - Neat idea, love the concept but the follow through is heavily slanted towards zergs
Auto gather - awesome.
The buildings can be attacked and destroyed in open world - Wait, what was that? So you're saying we're never going to have an extractor... What's stopping a 1200+ player alliance from just coming in and rolling over our maybe 6-7 players online at a time? Nothing, they will do it constantly and consistently just to grief us.
Where in the world do you expect these "smaller battles"? have you been in a red/black zone with these zergs? There is no such thing as a small battle. They will bring 10-30 people and just go zone to zone destroying the AOSilver resource nodes. Good thing you're making them cheap I guess, then we can just lose our hope before we lose our banks...

Change 2: Building territories
The current GvG attack declaration system is reworked
Each building territory will have a siege plot attached to it. This plot sits outside of the energy barrier
If an attacker manages to construct and defend a siege tower for a certain amount of time on that plot, they will get a standard 5v5 GvG attack on the next day
Of course, the guild owning the territory can also build a siege tower on their “own” plot, thus shielding them from an attack for that day

Change 2 - GvG Cock tease...
Small guild attempts to construct a siege tower to attack - gets zerged instantly and can't defend it - NO GVG
Zerg puts up their own "defensive tower" and defends it with 30 people - NO GVG
So after 2 massive hurdles that are easy for zergs to defend, we MIGHT get an attack... Good things our small guild all made plans to be there... kidding - NO GVG