My customization and combat desires tie into one another via my next talking point, which is a lowering of the importance of stats on equipment. What I specifically mean is that appearance should trump functionality more often than not. I don't want to wear a burlap sack just because it drastically improves my stealth rating. And really, a piece of chest armor can only protect you from bullets so much. There are other, more creative ways, in which equipment can be replaced by things like mutations and mechanical implants or straight-up cybernetic replacements. This is the future after all and such items would act as perfect carrot-on-stick replacements for end-game players.
What else besides awesome mutations and robot body parts would make a person excited for mid-game and end-game? Dynamic live-game events, with two or more potential outcomes that actually alter the game world in some way. Yeah, that'd do the trick. Sera recently touched on this matter and I think it's definitely something that's missing from most MMOs nowadays. But in this instance, it's truly worth all the trouble, because it blends two essential elements of both Fallout and MMOs: the ability to change a world through your actions and live, social events.
Additionally, the option of making participation a matter of microtransaction could be used. It could work like this: A live event crops up every month or two. For a player to participate in the whole deal, they're asked to pay something like three or five dollars. This purchase gets them access to both the entire arc of the live event and any resulting new content. The payment should still be an option after the event, simply for access to the new content -- although the price is best left the same, to encourage participation.
These are all things that, ideally, I'd like to see implemented well in the Fallout MMO. I'll be the first to say that many of them are potentially impossible, at least with today's tech. In time? Perhaps some of these ideas will come within reach of realization. For now though, I'd be perfectly happy if whoever ends up developing the actual game simply does their best at a couple of these features. Too many MMOs follow the same beaten path and while I'm all for better quality through iteration, it doesn't hurt to toss your pie high into the sky every now and again.