Anyways... To get onto topic with the recent comparison (and the first Kanto episode throughout the redo to actually get a complete comparison, in the words of Dogasu), I want to mention some of what I thought of the OOC things.
First off, in regards to how Misty is oddly calm. I think it would stand to reason that she would have some sort of calmness of the situation at hand, since, really, someone had to have led them off the ship, someone with nautical experience (like shipbuilding, for instance), and that experience would naturally go to Misty, hence giving her an advantage at the situation. Besides, she wasn't TOTALLY OOC, she did shout at Team Rocket during that sentimental moment, and she did threaten to throw Team Rocket's pokemon in the water (though, personally, I think she was bluffing, since she knew very well that throwing them in the water would probably upset the balance even further, and thus wouldn't risk it. Why they needed to place Koffing back in the poke ball isn't made clear, since it floats around anyways, and thus wouldn't really impact the balance [unless it touches the ceiling.].), and shouted at them to shake hands. That doesn't exactly explain the Gyarados plothole, but, then again, the whole Gyarados fear didn't really reveal itself until Johto (I mean, when she saw a gyarados banner in "Our hero meowth", she didn't even give a nervous shudder at the sight of it.). Plus, she was probably so shocked and horrified that she couldn't even begin to mention something more serious. Believe me, it happens. Heck, Vegeta in "Broly, the Legendary Super Saiyan" for example, was so scared of Broly that he couldn't say any more than "He's the legendary super saiyan", so even if she did know, she probably was too fearful to say it right (which is understandable, since if you were extremely fearful or nervous about some terrible thing, even you can get tongue-tied).
As for Brock's fiery personality, I think he showed hints at having a fiery personality prior and after this episode, and even afterwards. I mean, Other than his frequent "Charles Harper"-esque urge to womanize, in Bulbasaur and the Hidden Village, for example, when Misty was asking if Brock liked Melaine [in a bit of a teasing manner, but still], he hit her (twice, not to mention), and got rough on her. His reaction to Damian abandoning Charmander Definitely wasn't calm nor collected. Heck, in Johto, he even got into an arguement with Ash as to who should capture Donphan [even having Misty try to break it up, not to mention], and also arguing that he should keep Togepi since he raised it (which, if he truly was the pokemon expert/breeder he was, he would have realized that the key aspect of a baby pokemon's mother is that it believes it's mom is the first [living] thing it sees, and since Misty was seen first, then it chose Misty to be it's mom, regardless if he raised it or not.).
Meowth, well, the logical explaination of his arquaphobia is due to Hysteria. I mean, he was trapped on a sunken ship, with his own life at stake, and now they have to escape the ship by swimming up with seconds left, literally everything would freak him out, water or not. I mean, most of the other episodes involving him being near water never really had him in a life-threatening situation (being stranded on a (not even completely) sunken wreck visible above water doesn't count, since it isn't THAT much of a life threatening situation.), so the only possible explaination is that he was in a dire situation and had Hysteria flowing through him)
As for Pikachu being a Jerk in this episode, considering how he acted most of the time of that season, he was kinda on-character here. Besides, he was working together with Meowth, which, considering how Meowth acted to him, was explainable, not to mention was the first time.
Also, the Onix thing was kinda explainable since they rushed up at their max speed (as evidenced by their "Come on, lets go!", and their running up Onix.)
Also, yeah it does, but that doesn't mean they can't survive it. Also, speaking of Dragon Rage, in the episode "Fire and Ice", Arcanine used Dragon rage, and it was only a small whirlwind, not the water/tornado that we saw, which hints that A caught pokemon's abilities might not be as tough as if it's wild (or at least, it's not powerful enough, since Arcanine is definitely not nearly as powerful as a Gyarados, generally speaking, even without type comparisons.).