Now Worst case Scenario was a good episode, but here is the problem, it was set in the Holodeck instead of the real world. Its like the Maquis federation tensions had become such a non issue by season 3, the only to explore it was through the Holodeck.
That's part of the tension between the creators and the network that I mentioned before. Because of the network restrictions, the only way the writers could tell the kinds of stories they wanted to tell was through things like holodeck simulations, alternate timelines, duplicates of the crew, and the like. In episodes like "Worst Case Scenario," "Before and After," "Year of Hell," and "Course: Oblivion," you can practically see the writers straining against the restrictions, telling the kind of major, consequential stories they wanted to do but keeping it in contexts that would let them reset it all by the end of the hour.
The Maquis didn't have nearly enough of an impact on the series to justify their presence in the first place.
Because the original idea didn't work out as they intended, due to the network's policies. It's not unprecedented. A lot of things about TNG's original conception fell by the wayside due to producer changes. The
Galaxy-class
Enterprise was designed for deep-deep-space exploration, had civilians and families onboard so it could function as a whole community in space without needing external support, and had a separable saucer so the civilians could be left behind before the ship went into combat, but that all ended up being ignored in most of the series, with the ship mostly on diplomatic, political, or relief missions and the civilians being all but forgotten. And once Geordi became chief engineer, his VISOR became an almost irrelevant part of his character, except when some outside force co-opted it.
This sort of thing can happen with TV shows for multiple reasons. The creators may have ideas that they initially intend to develop as a major part of a show, but then once the show is in production, some of those ideas may end up falling by the wayside. Nobody can really know in advance exactly what will happen when a show goes into production, so plans will inevitably change.