I like the complex long-reaching arcs, too, but there's definitely something to some of the episodes in TNG. In one episode, for instance, Picard is captured as a Cardassian prisoner of war and the whole episode is torture and interrogation focused entirely on breaking Picard by any force or temptation possible; in another, Riker switches between a reality where he's a mental patient similar to Sisko's adventures in the early twentieth century (less the religious parts). These are self-contained 40-minute stories, but they're still very interesting. They're less sophisticated in the way that the Twilight Zone is less sophisticated, but that doesn't mean they're bad.

I will agree with liviconnor, though: You can feel free to forget the episodes where Riker doesn't have a beard, though. And, for the most part, though, it sounds like you want Enterprise, which is better about long-reaching arcs, especially the later seasons.