"New" Enclave
BoS
NCR
Caesar's Legion (maybe)
Mutants (Master's Army Remnants)
Factions (Minor):
Great Khans
Viper Gang
Jackal Gang
Follower's of the Apocalypse
Casino/Mob Bosses
Merc. Organizations
Factions (Miniscule):
Raiding Parties
This takes place in the next 10 or 20 years: As an enemy similar in nature and technology to that of the old Enclave rises on the West coast, all the factions in the area must unite to fluster the plans of murder, expirimentation, and kidnapping of entire settlements by this enemy. (Confrontation of this enemy not meant to be extended, as it only represents a fraction of the game.) As they accomplish this goal, the factions offer many quests in their efforts to rebuild. After a set number of in-game days (or realistically weeks), the reconstruction efforts are automatically complete and the quests available during reconstruction are renderred obsolete. In the time after the defeat of this great enemy, the player may take militaristic, peaceful, or uninvolved action for the rest of the playing time.
Faction options/interaction - military: The player will be given the choice to join up to one major, and all minor factions at one time throughout the game. You will have the option to grow the faction you are involved with through force or peaceful action. By peace all factions flurish in harmony and develop steady trade relations. By force, you may ally with other factions against any factions of your choice, take on only a select few, all at once, or one at a time. You will be able to declare peace and war at any time. this is not a strategy game, so you will only be able to select cities/settlements/bases to attack then choose between leading the battle (a large group of soldiers follows you), being led (fight alongside troops as they move with free will), or observe the battle from a free movement - distance from battle restricted - spectating camera.
If a battle is succesful, a simple presence of your faction in that settlement/city/base occurs. If at war, enemy factions can attack your cities/settlements/bases at random times. Also, if wearing your faction armor at any time in an enemy's territory, they can fire at will. Attacks are mounted by talking to your faction leader about wich settlement/city/base you want to attack and from where. You then report to your settlement/city/base commander and inform him to launch the attack. You then procede on foot without loading screens or fast travel to attack the designated target settlement/city/base. The battle ends once all combatants are dead and a notification appears.
Faction Peace Time: This time is much like the old wandering the wastes fallout idea ... it is recommended to players who like to wander/explore without being shot by an enemy faction.
"New" Enclave: After the Enclave reaches its breaking point, it uses its remaining resources/equipment to enlist new troops and develop somthing near to a nation. In desperate times, their philosophy changed and they slowly learned to accept mutants, ghouls, and the indigenious population (Wastelanders). They aren't quite as large as NCR, but make up for it in technology, knowledge, and equipment. They have ELECTED for once on a President worthy of leading their new Democratic government. They quickly grow in size and popularity in this ever-changing wasteland.
(Explanation for the Enclave's return and why they'd want a wastelander as a recruit, and maybe soon a leader.)