There are a bunch of long-running series that make (or made) heavy use of filler content of, let's say, variable quality (Naruto, Bleach, etc.). Other than those, I have a couple that spring to mind:

• Recency bias might be factoring into this one but Ryza no Atelier. I just watched the final episode literally within the past hour and it feels like such a let down compared to the penultimate episode. We go from a huge boss battle to a peaceful scavenger hunt. It just seems like you had an obvious place to end the show on a climactic moment in which the protagonists overcome adversity and realize the beginning of their heroic ambitions; but instead we devote the entire final episode for some kind of moral lesson about farming and friends? Don't get me wrong, just cutting the final episode won't make this show actually good, but it would at least be improved; meeting the requirements of the post.
• Carole and Tuesday: I really liked this show, but I feel like the story could have been more focused. In the final third or so of this series, I feel like it rapidly expanded the scope of the show to the detriment of being able to focus on the main cast's story.
• Planetes: I might make some people mad with this one, but I really liked this show when it focused on the space garbage disposal bits and much less so when it forced a romantic relationship between two main characters. It didn't really feel earned and, frankly, the relationship focused a lot on reinforcing traditional Japanese gender stereotypes and left a bad taste in my mouth.
• Clannad: If I didn't make people mad with Planetes, I have certainly made some mad with this one. Full disclosure up front, I have not fully watched this series, so if some Steins;Gate level twist makes all the rest of the show great, then so be it. I just felt like the story would focus entire episodes on people/things that just ended up never mattering again going forward. I remember after a couple episodes just thinking, "What was the point of all that?". It has been a couple years since I gave it a shot, so I don't really remember specifics, but this one could really have used some editing. I imagine the movie version helps this problem, but I haven't seen that after what I experienced with the show.