Salutations! Well, I read through some of your work and I've got some feedback for you!
To start off with, there were two things that struck me when I started reading: your prose, and some of your uncertain details. To begin with, as a reader, I'm not as invested in the prose because all of the details feel like drive-by details. This happens when you've fallen into Passive Voice. Passive Voice has a number of causes (adverbs AKA: -ly words, being the most prevalent) and one of the causes, in your case is the use of -s instead of -ed. This is a notoriously tricky kind of prose and it's very easy to fall into Passive Voice when using it. Now, that doesn't mean it's impossible to use, however it is difficult to keep your voice Active.
Usually this kind of writing is used in stage directions and scripts. To expound a little: Passive Voice is what happens when you tell instead of show. As it happens, your story has an exciting premise, but I don't FEEL the excitement through the narrative. Instead I feel like I'm standing next to someone telling me they heard a story, rather than being in the story myself. I'll make an example using your text so you can see the difference in action when using -ed versus -s:
Original: On the Pyrus Dragon's deck the crew have already prepared for the countermeasures as a tall man stands near the ships wheel. He wears a pirate hat and an overcoat with brown hair down to his shoulders. A crew member rushes to the upper deck and looks up at him.
Edited: On the Pyrus Dragon's deck the crew prepared their own countermeasures. A tall man outlined by his tricorn hat and large weathered privateer coat, stood unfazed by Captain Julius's confidence and the roiling gray storm surging from the south, his hand on the ships wheel as though drifting through placid waters. A gunner rushed to the upper deck, soggy footfalls announcing him through the salt seasoned wind and patter of rain.
Now, my example is just that, an example. It's not perfectly edited or anything like that. However, I wanted to show you the difference between how a scene comes across in Active Voice, details just being there, and details helping your audience FEEL like they're there. To start with: you mention the weather very sparsely and I don't feel like I'm in it, so much as I've been given a weather report. So adding touches about a 'roiling storm' or even a 'gray' storm, can help immensely. You don't have to over-describe things to get that across either, just mentioning if there's cold, or a storm or, salt spray in the air, can have a dramatic affect on how your readers experience your story. Don't forget to use all the senses (Sight, smell, sound, temperature, etc.) to engage your audience. I want to FEEL like I'm on a boat with your crew, not feeling like I'm hearing a story second hand in the vein of "I had to be there."
Now, speaking of details, you'll notice I had bolded the phase "a pirate hat". I've noticed that your details are vague when it comes to the working of your ship. If you're going to be writing an entire novel that takes place on a ship, even for laymen, it helps to know your rigging, moorings, crew positions, and clothing. You don't have to get so detailed that you bore your audience with unnecessary facts, however, you need enough detail to make it believable as a setting. To start, "a pirate hat" doesn't tell us anything. Pirates didn't all wear the same hat, some had bandannas, skull caps, helmets of a sort, tricorn hats, Monmouth caps, etc. There isn't a single hat referred to as "a pirate hat" outside of gimmick shops and web stores. Every item of clothing has a proper name, as does every member of a ships crew.
Which brings me to the next part that I put in bold: "a crew member". Which crew member do you mean, here? Is it the first mate, the gunner, or the bosun? Using vague terms such as "a crew member" or "a pirate hat" tells me you haven't done enough research on your topic, and that is a turnoff as a reader. Now, this doesn't mean you haven't done research, however, as a reader taking this at face value, I wouldn't be able to tell that you had, based on the way the prose is presented. My advice is to research pirate crews, hats and clothing to start with. History, famous pirates, and pirate flag history. There are lots of nuances that, when ignored, can turn off a reader. Most readers aren't going to be the super history buff, however, people tend to read about what they're most interested in. With regards to things like pirates who had a very real and tumultuous history, impressive/horrifying historical figures, and a culture all their own cobbled together from all their respective experiences, there's a lot of flavor in the real history and readers will notice if the spice is missing.
Your own story doesn't have to reflect the history of the real world, if you've invented your own world or alternate history, that's totally cool! But the elements of reality sprinkled in will make your world and your characters feel substantial to your readers. To this end, another trouble I see within your prose also has to do with the action sequences. Again, I was still on the first page when the fight scene between Ryo and Captain Julius caused me to stop. Since you're sparse on the details of what's happening, and what you choose to describe are things passive of the action, rather than inside the action, again I don't feel like I'm in the story, and the image in my head isn't very clear based on your prose. Now, action is tricky stuff, you have to keep a pace that'll also keep your audience engaged, while giving enough detail to let us know what's happening, while not over embellishing and slowing down the scene.
Fear not, I'll make an example so you can see what I mean!
Original: The ship rocks as the cannon discharges and a large chunk of metal heads towards Ryo's ship. On the Pyrus Dragon Ryo catches a glimpse of the attack and his eyes widen.
"Men! Brace for impact." Ryo grips the rails in front of him and everyone else crouches down. Seconds later the cannon ball makes contact with the stern and obliterates the very back of the ship. The huge ship rocks and almost capsizes under the impact. With his feet under him Ryo speaks to a man near the main mast.
Edited: The Night's Tempest rocked as her cannon discharged with a thunderous blare, the aft-most end of Ryo's ship obliterated into splinters and metal shrapnel. The Pyrus Dragon careened to the side as the holes in its hull drank up the ocean.
Now, I know that I cut out a huge chunk of your narrative here, and I'll explain. First, I don't know if you've ever seen a cannon fired or what your experience is, but only in movies do you have enough time to shout to your crew and have everyone take cover before you're struck with a missile. Reality is, Ryo wouldn't have had the time to warn his crew about a new cannon that he'd been unaware of (as in the previous scene Julius was just unveiling this larger cannon). Now, if he'd seen a larger port-side window open up to unveil a new cannon through his looking glass, he could start adjusting his strategy. However, since none of that was established, he'd have been blindsided and unable to react in time.
Now, that's just the bit about Ryo being shot. There are other troubles in this scene as well. Captain Julius should not JUST be taking the tarp off of a new cannon. If you know you're going to war, you have all your men and artillery at the ready. You don't have men too scared to fire a cannon that they've been told they have as an edge over anyone else. Whenever there is new weaponry introduced into a battle situation, people make quick use of it to secure victory. They don't ogle and shrink away from the awesome piece of equipment that'll assure they stay alive on the open ocean. So that scene didn't make a lot of sense from a narrative perspective. To that end, the entire scene of the fight didn't make a lot of sense.
We open on a man who is the Pirate King, presumably because he's earned this position through his cunning and his strategy. He's waiting around for the other ship to get into position to shoot at him, rather than hailing cannons and gunfire on approach. This isn't very smart, so it undermines the character, because he's built up to be smarter than this from the get-go. Now, there's an easy fix for this issue: Start your story in the action. Don't start before the battle in a ship-to-ship stand-off, start your story with everybody already in the midst of shooting at each other. That way, it doesn't look like Ryo waited around to be shot at for no reason, Julius doesn't leave a tarp on the best weapon he has at his disposal for no reason, and it also could showcase how dangerous Julius is (by virtue that he's brought better artillery to the party) thus, also giving us some very real stakes to go by from the very beginning.
If you want your character to be viewed as cunning or smart, you have to show him doing the smart thing in battle. If I had a ship I would not wait for somebody to bring theirs around to broadside cannons before I started firing on them. Granted, cannons of different sorts have different ranges, but I'd be looking for solutions and consulting with my first mate and my gunners, possibly even my quartermaster about how we were going to tackle a problem. I wouldn't wait for the ship to catch up to me and then stink eye them from the bow. I'd be shooting! (Though, if I'm a guy who was low on ammo, I'd have to come up with another strategy entirely Lol, but that's another story) So, my recommendation for the beginning of your story would be to plunk us right into the action. That way, Ryo is already imperiled, Julius can show his might, and we're not left wondering why Ryo didn't do the smart thing and bail. (Sometimes being a good captain also means knowing when to retreat) We wouldn't know what happened, only that he's in a firefight that he's losing, and any number of things could've caused it.
So that's the battle scene. One thing that struck me about your work is that the pacing is off in some places. When the ship is being blown to pieces and Ryo calls on John to check the damage, the ship is already sinking, yet you have these two people having a conversation, rather than jumping ship. This also doesn't make sense, because in the time it takes to have this conversation the ship is already sinking and people are already dying. Ryo shouldn't even have this conversation, since he's a captain who can probably know when he's beaten, he should just be calling out that they abandon ship. John questioning this in the midst of the ship sinking also makes no sense. Why would he question this? They have no way to make a stand, and if he's the first mate, (which, I assumed because he's the only crewman who gets a name so far) then he should understand his captain's orders without explanation.
I know that this bit was used as exposition of Ryo's pirate code, but this is not the time or place for that. This is also not the time or place for Ryo to run to his cabin, as his ship is going down fast and he's still being shot at. He should be wearing his pendant because, again, pacing. If he's wearing it he doesn't have to rush to go get it, thereby using the moment to show his desperate escape. He's doing a lot of running around for a guy whose ship is sinking into the ocean in the middle of a storm (which would pick up the waves and cause the ship to take on water faster) AND being shot at. You have to consider all the factors you present when you're creating a scene like this. You introduced bad weather, an enemy, and a devastating power gap. You also have to consider real time. When Julius fired again, John wouldn't have had time to get people to lifeboats, come back, and get a few more words in edgewise to Ryo in the time it takes to reload and shoot a cannon. This slows the entire scene down and you run into the Christopher Paolini problem of bringing the scene to a halt, to have a conversation (or in his case, over-describe what everyone is wearing).
So, here's a resource on writing action/fighting scenes. This will help show you what I mean. Here's one for pacing so you have an idea as to why it's important. I also want to give you one for strong scenes so you can get an idea of how a scene can be shined up. I've got another handy tool: Editminion. This will help you a little with your prose, watching out for tricky adverbs that sneak in and detract from your action. To that end, have some prose tips and description tips that can really help with bolstering your roster of skills. I know it's a lot of reading, but it IS stuff you're going to need to know when you come back and edit your first draft.
Phew, okay. Now I know I only went on about what happened in the first post. That's because, as I read, the problems in the first post were the same ones that persisted later (and my feedback is already long as it is!) so anything that shines up the first post, will do the same with the rest. I will say that you've got an intriguing idea for a story here and I can tell you want it to be something adventuresome and exciting and I think that, you've definitely got that in you. You're already doing the right thing, you're getting your story down and you're getting it out there. EVERYBODY has to make edits like these when they first start a manuscript (and even after previous edits!) so don't worry, what I've told you about here is the same stuff all of us have to watch out for, and now that you know about it, that'll be easier to do! I think that you have some serious story potential and writing potential as well, and I hope that the resources I've shared help you as you go through your editing phase.
Huzzah, you made it to the end! (Patience level = 100!) I wish you the best of luck.