You can even see the changes in the introduction to the games. Personally, I love Pokemon because of Pokemon. I want to catch a bunch of Pokemon, show off my Pokemon, battle with Pokemon, and just generally explore and enjoy a world with my Pokemon. Maybe it's because I'm a genwunner, and RBY had a very simple plot, but I have /never/ cared about the story. However, the story in Emerald actually added to the experience. It made the game the best in the series for me. I don't feel like the story makes as much sense or is as strong without the player trying to stop both teams from awakening the legendary beasts. If they just remade Emerald, too, instead of both Ruby and Sapphire, they wouldn't have needed to add the massive waste of time that is the Delta Episode. It's so easy and boring with so much BS, and then at the end Zinnia's daughter is just randomly dead and idek it was literally the most ridiculous thing ever. I genuinely think that the writers have changed for Pokemon. If I see the word 'ideals' one more time, I will bust a nut. It made sense in Black and White, since the legendary Pokemon were representative of the war between realists and idealists, but that's the only iteration I tolerate that annoying repetition in. I definitely think by trying to make things more complex, Pokemon is both taking away from the complexity that was already there and confusing and boring the tar out of players. Why was Zinnia acting the way she was? Why did she seem like a criminal? To make her interesting or complex? Why? Who cares? Her daughter is dead because...? All the Delta Episode was was meaningless exposition explaining why Rayquaza can Mega Evolve. Does there really have to be a reason? Rayquaza is a Pokemon, too! Any trainer can catch him; he's not Jesus. It stands to reason that he could Mega Evolve because of the bond he shares with a trainer just like any other Pokemon. Plus, that stupid story changed the way Sootopolis City was formed by making it an impact crater rather than a dome volcano that erupted from the sea and then collapsed in on itself, making the new Sootopolis a geological near impossibility because it's an island surrounded by water! DEEP WATER nowhere near land! It makes so much more sense that it's a dome volcano- like what, when the meteor hit the Earth, the crater just broke off and floated away? You understand how ridiculous that is because crust doesn't do that. It moves because of tectonic plate movement, which is increasingly slow. Sootopolis would have had to have formed millions and millions of years ago, and if that was true, it wouldn't be so dang tall. It'd be round, with less defined slopes and interior. It is obviously not round nor near flat and people live inside of it, so the crater is new, making this theory totally invalid. The crust was also so dense in some places and so light in others that the middle sunk into the bottom of the ocean and the rest didn't? Crust is a consistent density, and wouldn't break off of a continent and continue to float. That doesn't make any sense. Did it hit just a really tall island? That would have made a free-floating island in the middle of the sea a mountain. That doesn't make any sense! Any mountain in the ocean by itself is a volcano! It had to have been formed by a hotspot, so it's just a volcano! It only makes sense for Sootopolis City to be a volcano- the Japanese know volcanoes very well, being surrounded by them and living on an island that was formed by just such volcanoes, one of them being one of the most famous dome volcanoes in the world with a legendary crater that I assume Sootopolis City was based off of. Well, I used to assume. I disregard this statement as being so unrealistic and so freaking stupid so I don't let it mar my opinion of Hoenn, since it's just not true.
(As you might be able to tell, I did not like the Delta Episode, lol. I thought it was a good experience farm, though. >>)
Team Magma and Team Aqua were good in Emerald because they were fighting each other, too. You can see snippets of that in ORAS, but it doesn't really come off that way because you never really have to deal with the other team. The combination of Team Aqua and Magma trying to make the world better for people and Pokemon in different wrong ways and also having the added motivation of competing with each other and going about this in a criminal manner enhances their characters. Plus, without fighting one of the teams, where in the other game things are going on with that team, nothing is going on in your game, making that area of the game /utterly boring/. Lavaridge Town(Jagged Pass), the Mossdeep City Space Centre, and Mt. Chimney meant almost nothing to me in this game because I didn't have to do really anything over there (until the aforementioned trainwreck Delta Episode). Also when Kyogre and Groudon lay waste to Sootopolis and have to be stopped by Rayquaza, Maxie and Archie change and become friends because Rayquaza represents unity, balance, and 'calm skies' between harmonious, similar bodies like Land and Sea. In a maybe helpful analogy, Rayquaza is the Avatar, and Maxie and Archie's teams are both the Fire Nation. I'm probably making the story out to be more than it is, but I believe that maybe unwittingly, Emerald's is the best plot (next to B/W) in the entire series. ORAS doesn't have any of that. I like Steven and all, but he's everywhere because he's a rock expert and they have to integrate Mega Evolution into the story somehow. It's actually really annoying to be literally harassed by Steven and his exposition dumping throughout the entire story. Also Sea Mauville and New Mauville. *Loud sigh*.
Sea Mauville is almost as good as the original Abandoned Ship, though it's not nearly as randomly discovered and optionally interesting. I love the inclusion of Professor Cozmo's story and his relationship with his father. That is how a backstory should be done in games like this- I should listen to it by choice and come across it organically. Cozmo is such a random character to have this for, too, but it adds to the world. It makes the NPCs seem like real people, and I wish we had gotten more of that throughout the game. I missed Mr. Briney, I feel like I only was with the guy for 20 minutes when, in the originals, I was with that guy all the time (probably why that Route with the Abandoned Ship is so surreal when surfed on). Him and the sidequest in which the player rescues Peeko was so memorable in Emerald that I named some of my Pokemon, Nintenpets and other little companions "Peeko" since playing the game. It goes by too fast in ORAS, it all does. A story that paces itself well is much more epic than a story that explodes with action, ORAS. Also, why the shoutout to Kalos? That was not in the original, kids. They still decided to make Mauville City a gimmick at any rate because reasons, and I was really ready to throw the biggest fit in the world. It's safe to say that in ORAS, the story is nigh ruined for me.