Here's my idea for a Fallout multiplayer system:
think that it should have a maximum of 4 players, and would work like this:
No player can just enter/exit the game and let the other player continue playing. The game you start with a specific other person can only be continued with them. This way, it ensures player experience/level balance, sort of like D&D. All player characters should get mutual experience for kills, albeit slightly lower depending on the damage you personally dealt to the enemy.
I fully endorse this style as it would make the game excellent for guys who like to play co-op games with their girlfriends or a group of their friends(ahem, me). This also allows some characters to not be combat oriented and have their pals defend them in a gunfight, while that person serves as the tradesman and negotiator when dealing with NPCs. This style of playing allows Fallout to retain its traditional system of quests and combat, and encourages teamwork. However, if the players decide they want to split up for some time and operate solo in the game world, this would be allowed as well.
The teamwork element would also add a variety of perks to the game for when the player characters are within a certain radius of each other (IE damage bonuses, merchant discounts, accuracy bonuses, and so on)
These perks can be selected from a list when total player level sum reaches certain points depending on how many people are participating in the playthrough.
For this to work properly however, VATS would have to be removed from the game and there would not be any game pause when speaking to other characters or bringing up your pip boy.
I understand that it would be difficult for certain audiences to be able to coordinate "play times", but I think that this is the best way to do a Fallout MMO while still retaining it's core elements.