Why is it necessary to diss the Nexus Force so? They're not that bad, you know. Remember the Faction Leaders? They were kinda nice. I'm sure there are other nice people around, too. Seeing as, after all, they're trying to save the world. I'm not saying they're perfect, but continuing to act in this way even after so long and explaining it as laziness just doesn't do the trick with me.
After the Faction War ended, perhaps it took some time to undo this regulation, but eventually I'm sure things would go normal.
Besides what does it even mean to be a Limited Recruit? Why is one a Limited Recruit and how is it decided that one should be Limited? The only explanation I can see is that it's Recruits who haven't yet risen to Rank 1 and therefore are considered unfit to move on to more dangerous areas. However, with further training everyone should theoretically be capable of moving on to the next stage. Plus, if the Force has a constant influx of new Recruits it wouldn't really need to keep the old ones back at Avant Gardens, seeing as the new ones could defend it. Moreover, making sure other places are defended would be even more important.
Furthermore, if you consider that the Nexus Force in this world is an actual military organisation and not something in a game, the player's freedom to go wherever they wanted is an element that could be restricted heavily, if not removed entirely. If the Nexus Force assigns posts to its members, then it doesn't have such a problem. In fact, if you think about it, even in-game it does have people with assigned posts. Everyone else but the player. It's only a matter of not handling the Multiplayer aspect of the game into the story well. With so many players following a story that is often designed like a Singleplayer game's story it seems like everyone is roaming about when in fact the majority should act like the NPCs do.
Including game mechanics in a story is a dangerous path and if walked carelessly it can lead to the Dark Side of the Force.