The modern insight is that Mary Sues aren't strictly a problem of characterization as much as they are a problem of story structure; it's not that Mary Sue or Marty Stue are particularly powerful or good-looking, it's that the rest of the story bends its internal logic solely to showcase how cool and good they are. (Of course, you could argue that EVE isn't exactly innocent of this, with its new-NPE and constant harping about "immortal demigods," as opposed to "dangerous and insane mercenary types with cloning equipment.")
The main problem I'm seeing is that it's hard to find something that's relatable for a capsuleer to do with their lives. Most of the classic threats and motivations at personal scale either aren't a problem because clones, or fix themselves when you throw a bunch of money, mercenaries, or high-bore starship artillery at them. The answer to most personal moral conundrums is "rip out your plugs and retire on the money you've made so far, because there's nothing in the trade but shedding oceans of blood, no matter which side you're on." There's probably a literal hundred little factions to be a part of, and nothing to unify people identifying with them working towards some common goal. And so on.
There's always interpersonal drama, or taking the struggles in the actual game in-character, but that tends to get soap-operatic in a hurry, I've found; interpersonal stuff without further context is very hard to do right, and a lot of people are really poorly equipped to deal with conflict when playing for keeps.
(You're not alone in thinking that it might be cool to explore the setting from a baseliner point of view; until RL intervened, one of the MITG guys was working on a Storyteller-powered game set on the wormhole citadel.)