I just think cover stories are the way to go because they're basically canonical filler–you can't go wrong. Some of the stories can be padded and they explore other character's journeys as opposed to just pitting the Strawhats against new enemies, which they definitely have no shortage of.
Anyway, I find that the best filler arcs strike a balance between bold storytelling and [not]cannon-breaking, while possibly expanding on ideas not covered in depth in the manga. For instance, the 3-Tails Jinchuriki filler arc in Naruto Shippuden introduces an unknown Jinchuriki, takes the liberty of writing his back story, expands on Naruto and Jiraiya's relationship (and even animates some graphic-novel cover art) before the latter's eventual death, and shows how the Akatsuki captures him in the end. The filler is essentially canonical because they take something from the manga and fill in the gaps with an original story.
A filler arc might feature a powerful antagonist who poses a very real threat to the Strawhats and the greater world around them, while tying in the story with canonical characters, events, and unknown back stories while not treading on the cannon material or creating plot holes. As opposed to just dishing out new fodder villains who are just a pain in the butt more than anything–whose actions are obviously of little consequence to the Strawhats or the story at large other than the crew wading past enemies to simply get where they need to go.
They could involve important characters like the Shichibukai--and even if they don't go so far as to get Oda directly involved with the story telling, they can at least avoid cannon crushing plots or uncharacteristic representations of its characters by getting his input on them. They can even create recurring filler characters (friends and enemies alike). And while I'm not a huge fan of interweaving filler and cannon because I feel that can damange the integrity of the original story, there can still be some level of acknowledgement that those filler arcs happened later in the series. Whenever a filler story arc ends; all the people, places, and experiences the characters had are forgottten and never mentioned again. That makes the series feel superficial. If there's ever a flashback montage of all the struggles the Strawhats have endured, they might include an excerpt from a filler story. Or characters might be reminded of something that happened in them later on. But more often than not, the filler writers play it safe and just push out uninteresting episodes to pass the time. The writers should look at the One Piece TV series as a grand story and a work of art--and try to make every story count and stand on its own.
Some of the best fillers take bold liberties with the story's characters and unexplored plot points. They also nail the characterization. Some people may not agree with the decisions made in these types of filler stories but I feel they generate the most interesting plots when done right. The reason so many people skip filler arcs is because they're just boring, and more often than not the writers don't develop the characters or plot at all. While their capacity to develop the characters is limited by the manga, they can expand on the character development that's been seen and expected from the manga thus far.