Count me as somebody who hates such shows. Obviously I don't expect them to introduce all characters from the start within each episode, but the whole season-spanning epic arc thing has gone too far in my opinion. As a rule, each episode should tell a self-contained story that can stand on its own. If it also advances the main season arc a little, even better. But give me something that makes sense as a stand-alone episode, and I'll be so much happier.
One very concrete problem of the epic season-spanning arc disease is that it causes many episodes to feel like filler. When the writers don't strive to make each episode something that is interesting as a self-contained story, then guess what, each episode isn't interesting. In fact, such shows often feel like the writers stretched a two-hour movie out to 20 episodes. That's just plain boring.
This thread is mostly about science fiction shows, but let me illustrate this with a different example anyway: Buffy. The first few seasons were a perfect blend of self-contained stories per episode, that also often advanced the main season arc. Then in the later seasons, they got epic arc disease, and the quality just went horribly downhill - at least for my taste. The first few seasons are full of memorable episodes, because the writers obviously tried to make each episode interesting in itself. In the later seasons, the memorable episodes are very, very rare. In my opinion, that's just sad.
I agree with you to a point, that an episode can't rely on every other episode in the season to not suck. But it's a hard balance to strike, because a single 44 minute episode is not much time to tell a story in the first place, let alone a self-contained story and then also part of a broader story. But there aren't many writers that can write a story that takes 16 hours to tell (a standard American season), so you get filler wherever they fail. On the other hand, it's hard to develop characters much in disjointed one hour bursts, so a multi-episode arc gives some room to tell a complete story that doesn't feel rushed.