Interesting thread. Don't know if I have the strenght on commenting all I see wrong with Marineford and Fishman Island. But I guess I can go a little bit with the little changes I would have done with two other arcs.
Enies Lobby:
1. The reveal of the Eleven Jurors sucked
I mean I know that they just as the Houbantai weren't meant to be a big obstacle in the first place, which is a disappointment in itself. But I can let the latter slide. However the full reveal of the first juror was him literally laying down on the floor beaten up by Sanji which on top of things happened offscreen. A super unspectacular reveal after building up (minor hype) on them.
What would I have changed?
I would have changed it in a manner where at least the reveal is something worthy of the wow factor. Having them be OHKOed by Sanji could have remained. Heck, might even served as comic relief. But this honestly felt as if some pages were missing and I mean that quite literally. Back then I really checked again if the chapter was incomplete. It even didn't have 19 pages iirc.
2. Lucchi's lust for blood amounted to nothing
We had three instances showing that Lucchi is looking forward to fighting respectively killing Luffy. #1 He told Spandam that he enjoys killing which is why he is part of the organization as it makes killing legal. #2 Having an excited smile on his face when he saw that the Strawhats are ready to jump the chasm over to the Judicial Tower (for an uncharismatic bore such as him this is a strong statement). #3 Having a smug smile when he told Spandam that he expects Luffy to follow them through the tunnel as Chimney who he saw most likely reported the tunnel to Luffy. Again he seems to be looking forward to the fight. However in the end there was nothing of him enjoying the fight at all and he went on to preach about dark justice and the safety of the world and blergh. Not really in line with the three moments listed previously.
What would I have changed?
I would have made him get more excited as the fight goes on. I know that there's already plenty of characters in other manga that like fights. But not all are the same. Let's just look at Zaraki Kenpachi from Bleach and Hisoka from Hunter x Hunter. Both enjoy a fight and are yet different with one enjoying the more raw and brutal aspects of it while the other also enjoys the strategic part of a fight. I know that's very rudementary but I'm not here to talk about them. Just want to use an example on how enjoying a fight could be different. For Lucchi specifically I would focused a bit more on the killing/lust for blood part. He is a trained assassin. And from what we've seen his mastery of Rokushiki is far above the other CP9 agents'. I think it would have made sense to have him point out how much he enjoys finaly unleashing techniques that he couldn't use in the past 5 years because even if there was someone to kill at Water Seven on simple Shigan might have done the trick. Kinda like something like "But not you! You can take my attacks. You I can go all out against" or "Don't die on me yet Strawhat Luffy! I still have more deadly techniques I'm eager to show you!" And then as time progresses he could lose his cool to the classic "What else do I need to do to finaly kill you?"
I think Lucchi's personality would have benefited much from something like this. Plus it would have been some sort of payoff to the little build up previously mentioned. The fight itself is absolutely ok and IMO still perhaps the best one on one fight Luffy had in the entire series as Luffy and Lucchi were just beating the crap out of each other. It's just the dark justice preaching that leaves a sour taste in my mouth.
Thriller Bark:
1. General Zombies being fodder
They went down like nothing to Oars. But before that having a huge number of them seemed to already deminish their value compared to the previous chapter where only four of them were revealed. Especially with one being a sharpshooter which happened in the same chapter where Ryuma, the guy from one of Oda's previous one shots has been revealed to be part of the One Piece universe. I know I was not the only one thinking that the sharpshooter was Gil Bastar (protagonists of Oda's very first one shot). But then suddently you have two dozen of them. Instantly understandable that they would not amount to much.
What would I have changed?
I would have kept it with the four General Zombies and rather have those four show that the can stall the Strawhats a bit by themselves rather than their "sales point" being just armor and numbers. Especially since the sharpshooter and Captain John didn't have any armor (just like the strongest general zombie Ryuma). They don't even have to be on an equal level to the Strawhats but just showing that they are no pushovers would be enough for the Strawhats to focus on them so that the Spidermice and Tararan could do their sneaky stuff. Same result but with of a pushover feeling for the GZs.
2. Robin using clutch moves on zombies
I must admit that my memory is a bit fuzzy on this but I still have this written down as one of my pet pieves from back in the day so I guess it has happened. Why is this a problem? Well because they are zombies in other word dead flesh that is not moving because of fully operational body functions but because of magic (called DF powers in OP). One of the first things we see zombies in OP do is even having one lose a head and toss it like a ball in a joking manner. So using clutch moves on zombies should be totally pointless. It's ok if it dislocates some joints or even breaks some bones but at no way should it render the zombies immobile. It completely goes against what the zombies are established as within the story itself, creatures that feel no pain or fatigue. Of course if you're bones get pullversized as with what Oars did to the General Zombies or with what Luffy did when he shattered part of Oars spine then it's a different matter as even if they don't feal pain (even though for some reason the GZs were moaning as if in pain) the bones are too broken to make them move. If you literally pullverize the bones, then I can get behind them being immobilized. But that's not what Robin's clutch moves do.
What would I have done different?
Making this actually a focus point. Have Robin discover that her "speed and strenght mean nothing to me" statement can only take her this far. Saul himself told her that the sea is fast. And while he meant this in context with her at some point finding companions would have been a nice way to tie such a world view to understand that there will always can be opponents that are not phased at all by how she fights. I mean now after the timeskip she's using stomping attacks. Wouldn't it have been a nice idea if the zombies would have made her realize that for some oppenents she just needs to completely rethink her attack set? I would have used it as a trigger experience to develop such attacks that we see now as normal.
3. Jigoro and Dogpen being tricked to jump out of the window
Honestly that was such a poorly written part I was amazed that it was even greenlit. I have no problem with them being tricked into jumping down but the how was pathetic. Robin somehow finding the right words to make Hogback accidentally spout such a ridiculous command just seemed like a "well, I'm out of ideas" moment from Oda. I don't know if it makes more sense in Japanese but in English it just totally doesn't make sense.
What would I have done different?
Rather than tricking Hogback to trick Jigoro and Dogpen into jumping out of the window, I would have cut the middleman. Both hate each others guts and everybody in the Strawhat crew knows that. So it should have been easy for Robin to use Zoro's and Sanji's animosity to her advantage to make their respective zombies jump to one up their rival instead of it being the result of Hogbacks command. Would make the situation seem less like lazy writing and more something that only people with good knowledge of their crewmates could pull off.
4. "You must be triggering the bazooka with your thoughts"
Does this even need an explenation? I still hope that this is either a) me remembering things bad or b) being a totally bad translation. So if it is, please ignore this point. But if not then WHAT THE ACTUAL HELL? Since when was it established that we have weapons that you can actually trigger with your thoughts in the One Piece universe? I mean if we go there and establish this as something that the ancient civilazation or Vegapunk could have developed, then I'm willing to accept it. But it has to be introduced properly. When we heard that Lasso is a gun that ate the dog fruit it was also a WTF moment. But at least Usopp made a point that this doesn't make sense. And later with the introduction of Vegapunk we at least know that he's developing things like this. Still iffy about the exact mechanics but at least it's pointed out as something special and not brushed aside. But holy hell, here Sanji just randomly mentions that Absaloms bazookas are triggered like that as if it is a completely random thing to happen in the OP world and that's it. Sorry, but that's bullshit.
What would I have done different?
This one is actually very easy to fix. Simply have the bazookas have triggers in front of Absalom palms matching/complementing the move his hands are performing when he's pretending to actually fire from his hands. I mean the bazookas are friggin invisible so there's no reason why there shouldn't be some invisible triggers there. Make it a custom build made for the sole purpose of Absalom being able to put on this show.
5. Oars' injured arm
This also doesn't make sense with what has been established in the arc about how the zombies work. Just as stated in point 2. the zombies are meant to feel to pain or fatigue. Their bodies are not reanimated because of their organs and body functions being biologically revived. They are dead flesh, moving with magic (DF powers). Oars' arm suddenly not moving anymore because it is too beat up doesn't make sense. The arm aswell as the entire body is DEAD. It doesn't get more beat up that this.
What would I have made different?
Surprisingly this would have also have had another solution that actually ties in much better with what has been established in the arc previously. Remember the zombie who's head fell off I mentioned earlier? Did it hurt him? No. Something similar could have been done with Oars' arm. Make the Strawhats deal the damage to the arm. But when it gets to Oars actually using bazooka himself make him realize that actually the arm in question fell off. He's a zombie and doesn't feel any pain. So it's believable that he didn't feel it. Also it could have made for some comic relief having his arm move doing the bazooka movement only to run into his legs. I mean there's countless of zombies where we see just a detatched zombie arm crawling on the floor. So it's much easier to believe that this is a thing that his arm being too injured to move.
6. Too much I miss Laboon in Brook's flashback
I know how deep the connection between Brook and Laboon is and I have no qualms with the connection. But he mentions him far too often in the flashback to a point where it's just not natural and just there for Oda to hammer the point home how much Brook misses him. I mean how often in the series have seen the Strawhats say they miss what/who they left behind? Sanji remembers Zeff only when it's relevant to what's happening like Zeff's life being in danger or how he was raised by the old geezer. He doesn't go on about how he misses him. Usopp doesn't go on about Kaya and his former "pirate crew", Franky hasn't mentioned the Franky Family a single time since he left even though he wanted to stay in Water Seven to protect them. But Brook mentions Laboon more often within this short flashback than all the Strawhats combined reminiscence about who/what they left behind. Seriously, if you miss Laboon so much, why did you go on with your voyage in the first place? There's no agency to his adventure at all. What's his goal? I only hear him go on about Laboon.
What would I have made different?
Making him shut the fuck up about Laboon! Nothing more needs to be said on that matter.
Well this is it for me. Sorry for the large post. Didn't expect it to be this long.^^' If you don't have any problems with what I discribed all the power to you. But those things really rubbed me the wrong way. And I actually enjoyed both arcs a lot.