I tried to look at this from both types of players, those that like the care bear style (no offense intended) and those that like the ffa pvp no safe zone type of players.

The basis of this outline is to distinguish what a conquest tribe and non-conquest tribe can do. (it is not meant to determine how an actual siege will work)

Conquest Tribe
1. Can control an unlimited amount of contested totems (limited amount of non-contested totems)
2. Ability to set a capital totem within the zones that were live on official launch day - this totem cannot be seiged
3. Can be attacked on any owned territory
4. Asset damage can be done to structures at any time including the capital
5. Sieges must be initiated by whatever siege system is implemented
6. Capital city cannot be seiged
7. Initiate a territory trade, purchase, hand off etc (territories can be sold this way to other tribes)
8. Ability to decline or accept a trade, purchase, hand off etc
9. Only an official tribe leader can initiate a trade, purchase, hand off etc, if the trade, purchase, hand off etc is accpeted the territory is placed under this tribe owned by the requesting tribe leader.
10. Only the initial tribe leader who placed the totem can accept or decline a trade, purchase, hand off etc (prevents griefing by stealing a tribe by the members)
11. If a territory trade, purchase, hand off etc is unanswered after 7 days, it is automatically declined.

The following is based on a siege system and would be adjusted according to whatever siege system is implemented This is just how I think it could work
12. Sieges can be initiated by those with proper rank (through whatever siege initiation system that is implemented)
13. As soon as a siege is initiated the tribe leader will receive an instant message if logged in, if not logged in this message will popup on next login.
14. A message will read, "Your tribe has been seiged, click ok to continue or click surrender to initiate a 24 hour countdown to a handover" or whatever, something along the lines of that
15. The siege will start in exactly 24 hours from when it was initiated. (again this would be setup however a siege system is implented)

Non-Conquest Tribe
1. Can control a limited amount of territories within non-contested zones
2. Ability to set a capital totem within the zones that were live on official launch day
3. Capital city cannot recieve asset damage
4. Capital city is a safe zone
5. All other owned territory can recieve asset damage at any time and can tribe members can be attack on the territory
6. No controlling territory can be sieged
7. Initiate a territory trade, purchase, hand off etc (territories can be sold this way to other tribes)
8. Ability to decline or accept a trade, purchase, hand off etc
9. Only an official tribe leader can initiate a trade, purchase, hand off etc, if the trade, purchase, hand off etc is accpeted the territory is placed under this tribe owned by the requesting tribe leader.
10. Only the initial tribe leader who placed the totem can accept or decline a trade, purchase, hand off etc (prevents griefing by stealing a tribe by the members)
11. If a territory trade, purchase, hand off etc is unanswered after 7 days, it is automatically declined.

Penalities for asset damage
Any member of a good or neutral tribe attacking another good or neutral tribes assets would be treated the
same as attacking another good or neutral player with whatever alignment system is implemented.

With something like this in place and a totem decay system it would make for a very exciting game.

I know there's going to be flaws, so let's find them and fix them.

Edit: Added after original post based on feedback
1. All areas outside tribal territories will still have the same FFA PVP rules as now based on the alignment system when it's implemented.
2. Setting yourself as a conquest or non-conquest tribe would be just like setting your tribe alignment, once it's set you can't change it without disbanding your tribe and resetting your totem.
3. A conquest tribe could have any totem seiged at any time, so you would have to be carefull about how you split your forces - this would control how many conquest totems you place.

The problem with this system
1. Capital cities controlled by non-conquest tribes can be a used as a safe zone for not only themselves but can allow other pvp'ers access inside their walls when being hunted by other pvp'ers
2. Non-Conquest tribes can setup a 2nd tribe next to their capital that is non-contested that is used as their Conquesting tribe. - the members can jump back and forth between the 2 tribes