The biggest question for me is - how not to make Charisma a dump stat? Other main statistics and most of the skills can be transferred to a MMORPG without major problems, but Charisma in Fallout games was pretty much all about interacting with NPCs, while MMORPGs naturally focus on interaction between the players, making Charisma's original use less useful.
In single-player Fallout games, Charisma influences two skills - Barter and Speech, both of which would be pretty useless with PCs, and while still having their uses with NPCs, limiting Charisma to that would make it a dump stat. While IMHO it would be good to keep that original use as well, I think merging Barter and Speech into one skill that governs all interaction with NPCs could make it at least less useless.
Another idea is to introduce a Leadership skill, which would allow your character to temorarily boost the skills or stats of his friends. It could also help you gain ranks in a faction more quickly, if a faction system where you can gain ranks within them is implemented.
As for perks, I'd like for Chris to, just like J.E. Sawyer did for Van Buren, dump level requirements completely and make all perk requirements skill and stat-only. It will give you more incentive to specialize in a given skill, as a high skill level would give you access to more powerful perks.
Any other ideas on how to improve SPECIAL or make it more suitable for a MMO? The Vault - Fallout Wiki * Fallout Online * Fallout IRC Channel * Fallout: New Vegas