This is all sounding very good
sorry, I havent read all 15 pages but.... (shamless I know)
some ideas; you NEED new animations for the zombies, ive seen them put into M&B before where they are just slow naked peasants, it doesnt work.
survivors need to be few and far between, most if not all people who join your party should be companions, or at least you need to be able to equip them, adding to the feeling of scavenging for parts.
zombie controlled settlements need to be raided, but not just an option that does it for you like in M&B, you need to enter the town, killing zombies and perhaps taking food/weapons out of crates (that act like chests) in the town/mall/whatver.
the vast majority of locations should start as zombie controlled, allowing survivors and the player to take places as hideouts.
you need lots of buildable upgrades to your hideout, to make having one main safehouse a better option that just taking everywhere.
slowly degrading items? - makes more of an insetive scavenging and stockpiling supplies. - to go with this would be non permanent ammo, meaning that when you buy one set of ammo it wont magicaly refiill after each battle (perhaps 4-5 battles worth per bundle, not depleting if you dont use the ammo though)
LOTS of zombies, 'lords' of the zombie faction (would probably be the big boss zombies you mentioned) should have massive hordes, realy realy massive hordes. dont worry about it lagging- the reinforcement system will make them come in waves.
most humans will take you as prisinor, or just loot you and let you go when they beat you in battle. zombies wont. you should have a chance of escaping the battle if lost, droping some items and losing companions. otherwise you will die (or become a zombie?) might be a bit annoying, but i cant think of a better system.
EDIT: allso, please dont make it TOO serius, by all means make it a dark and gritty bloodfest where we will all ulitmately die horribly, but have a laugh whilst your doing it (see Left 4 Dead) afterall, the reason so many people love the idea of zombies (in games obviusly P
is because they are so goddamn fun.