Some ones that I don't think have been mentioned yet:
Ginny's time at Mariejois.
-This is probably WAY too dark for the manga to ever actually show. But....man, it would give us some interesting insight on what's going on. How she got captured. Who her husband was. What Saturn's experiments were trying to achieve. There's a really interesting one or two volume manga story in here. Even if it would be the ultimate downer, I think it'd just be interesting to see.
The Fall of the Oykot Kingdom.
-AKA Nami's origin story. I don't know, it's just a little strange that we don't even know who the Marines were fighting or why. I just think there's a interesting story waiting to be told here. Were the Marines just fighting pirates, or were they trying to capture the Ancient Weapon Uranos for themselves?
Enel's Conquest of Skypiea.
-It'd be kind of interesting to see Enel's rise to power. It might be VERY short, since it can probably be summarized as "And then he used lightning", but still.
Enel's Adventures on the Moon for the last 2 years.
-I mean, maybe it's just all Enel sitting and ordering his robots around. But, I'd still take a few chapters showing us what Enel's been up to since the timeskip. Maybe he's been fighting off wave after wave of Space Pirates? I don't know, you could do SOMETHING with this, surely. Maybe Enel's started to conquer the other planets or moons orbiting around the One Piece World?
Crocodile pre-Baroque Works.
-I just think it'd be interesting to see why Crocodile ran away from the New World. Plus, we could find out what he owes Ivankov.
The Construction of Thriller Bark.
-When you think about it, turning a graveyard into a floating island is kind of a engineering marvel. And I have NO IDEA how Moria pulled this off. How'd Moria find the graves of the former Rocks Pirates? How'd Moria find Oar's body? There's a STORY here.
Shanks returning to Mariejois after Roger's execution.
-We might eventually get this. But, I just kind of want to know how that went for lil' Shanks.
Bege's adventures on the upside-down island after entering the New World (Chapter 594).
-I'm a little surprised this never got mentioned. I think a lot of people still think this could be Uranos. I don't think so myself. But, honestly, I would take a short story about ALL the Supernova's adventures on the weird islands that we skipped over. Urogue on Raijin Island included.
Smoker's quest for his Mystery Cube.
-Again, we might eventually get this, whenever we explain what Smoker's been up to since Punk Hazard. Still, there's a story here.
Bon Clay surviving in Impel Down.
-Again, there's a story here. And, also again, we might get this whenever Bon Clay shows up again in the story.
The event that caused Fujitora to stab out his own eyes.
-It might be too dark to show in the manga. But, again...there's a story there.
Kuma's adventure on Amazon Lily.
-I mean, he HAD to have gone there, in order to send Luffy there with his Paw-Paw powers. But, that's the ONLY place we didn't get a scene of Kuma visiting during his flashback. It's just a odd omission, and chances are Oda skipped it for a reason.
Blackbeard's attack on Drum Island.
-We still don't know why Blackbeard was on Drum Island in the first place. It'd be interesting to see why he went here.
Blackbeard's attack on the Revolutionary's base Baltigo.
-Again, we don't know why Blackbeard did this. And with THIS event, it could make for a really interesting fight.
Shirahoshi's birth.
-I'm just morbidly curious. I mean...*gestures over to how smol Otohime is*. And...*gestures over to how hyuge Shirahoshi is*. Just...how? Plus...maybe we could show how Shirahoshi got "chosen" to be Poseidon?
SWORD's origin and formation.
-I just think it'd be interesting to see how this organization got it's start. This could be a interesting "spy" type story.
CP9 rejoining the World Government after going AWOL and rejoining as CP0.
-We did get a SBS answer about this. They uncovered a secret plot. But, I wouldn't mind this getting expanded into a filler arc in the anime, or something.
The Germa Empire's 66 Days of Rule and the Conquest of Four Nations.
-We might eventually see the 66 Days as part of the Void Century flashback, maybe. But, again, it'd just make for a interesting side-story.
Gin and Don Krieg's Travels.
-It'd be kind of interesting to see how they went from nearly dying at Baratie to getting all the way to Hachinosu. At least for a few chapters worth of story.
Pell showing up alive after the bomb at Alabasta.
-We never did get to see anyone's reaction to Pell being alive. I'd like to see Vivi reacting to finding out he survived the bomb explosion. Imagine him showing up just in time to attend his own funeral. Maybe we could get some gags out of everyone thinking he's a ghost.
Lulusia's history of Vampiric rule.
-I'm just curious why they were ruled by Vampires. How'd THAT happen? We didn't spend a lot of time on Lulusia, give me it's history in a chapter or two, why not?
Scopper wooing Ripley. (Or maybe vice versa?)
-It'd be VERY odd for One Piece to actually focus on a romance. But, this one I'm actually kind of curious about. I'd take a sweet little rom-com action story about these two getting together for the first time.
Roger wooing Rouge. (Or maybe vice versa?)
-Here's another love story I'd like to see get expanded upon. How do you fall in love with the King of the Pirates? How did Roger decide on Rogue?
Big Mom meeting her Three Eye Tribe husband (Pudding's father). (This one's...probably all Big Mom. Big Mom was the woo-er here.)
-Out of ALL of Big Mom's MANY husbands, this is the one who I'd like to see the most. Given how rare Three Eyed Tribe members are, there's probably a story you could tell, here.
The Love Lives of the Kuja Empresses.
-There's a lot of love stories that One Piece skips over, aren't there? Yeah, you know what? Just give me ALL of them. Make a one-volume collection out of it. Gloriosa. Shakky. Tritoma. Anyone else Oda wants to add (Maybe Joyboy or Nika had a relationship with the First Kuja Empress). All of them!
I guess what I'm saying is...give me a "One Piece...of Our Hearts!" spinoff manga!