New Hoenn Pokedex-There are 300 Pokemon in this dex, containing both new evos/prevos and Pokemon not there before. There's another case of a zeroth Pokemon(though not what you'd expect) and the other Hoenn event legendaries being 301 and 302
Hoenn trainersWinoa has a shiny Swellow as a nice cameo, and introduction to shinies
Hoenn Elite 4 Member Sidney-Absol evo(Dark/Fighting), Crawdaunt, Shiftry, Cacturne and Challenge Mode Zangoose
Hoenn Elite 4 Member Phoebe-Dusclops(rematch/Challenge mode has it evolve), Banette, Chimecho evo(Psychic/Ghost), Sabelye evo(Dark/Ghost) and Challenge Mode Shedinja
Hoenn Elite 4 Member Glacia-Walrein, Glalie, Froslass, Glaceon and Challenge Mode Weavile
Hoenn Elite 4 Member Drake-Salamence, Flygon, Altaria, Shelgon and Challenge Mode Kingdra.
Hoenn Champion Steven Stone-When teaming up with you to fight the baddies, he has Metang, Armaldo, Cradily and Solrock/Lunatone(depends on the version). When he is a Champion, he has Metagross, Aggron, Cradily, Armaldo, Skarmory and Claydol. If you get the event that accesses Deoxys, you shall be introduced by him and his father Mr Stone
Factory Head Noland-In a nice reference to the anime, Noland will be friends with an Articuno. It will be his friend, and in the Gold Battle it's the only Pokemon you can be assured to fight it. Its got the Hidden Ability of Snow Cloak
Arena Tycoon Greta-In the after-game, you first find Greta trying to get Brawly back into being a Fighting-type gym leader, and possibly take his place. Brawly will request you fight her-these two Pokemon are Medicham and Hariyama, each with their Hidden abilties.
Dome Ace Tucker-The ever-so fabulous Tucker is seen in the after-game in the main Pokemon contest. He is using an Arcanine. According to him, it has the ability Justified.
Pike Queen Lucy-Haughtily, Lucy will challenge you in a regular battle right when you enter the Battle Frontier. She will use squinty-eyed Pokemon in this battle with their Hidden abilities-Telepathy Wobbufett and Gluttony Snorlax
Spenser-Appearing after the villainous attacks to help the hurt people and Pokemon, he will recognise your kindness and give you a special item. A Venusaur NPC will follow him. This special item will allow you to visit Spenser's Sanctuary-a home of rare Pokemon found nowhere else in Hoenn. It has a Lv 60 Venusaur as a boss, with Chlorophyll. It was released by Spenser
Anabel-Anabel is found in the old Battle Tower, where an abandoned Lv 60 Metagross with Light Metal. It was released by Anabel
Pyramid King Brandon-In order to unlock the Regis, you must fight Brandon in the Sealed Chamber. While you can rematch the Regis, if you lose against Brandon here you can't catch the Regis, so save before you do. He will have four Pokemon: Solrock, Dusclops, Ninjask and one of the two Pokemon depending on the version. Pokemon Sapphire will have Sturdy Relicanth, and Pokemon Ruby has Pressure Wailord. After beating Brandon, there's a unique Lv 70 shiny Wailord/shiny Relicanth found in the Battle Fronteir waters
Wally-Gardevoir, Gallade, Roserade, Flygon, Magnezone
Your other rival(May/Brendan)-The starter you're weak to, Beautifly, Magcargo/Pelipper/Tropius(depends on the starter), Glaceon, Mighteyna and Altaria. In the after-game, she shall trade you a recently hatched version of your starter for her Lv 1 Squirtle with its Hidden Ability Rain Dish
Pokemon World Tournament-new membersProfessor Oak-Charizard, Tauros, Exeggutor, Gyarados, Pidgeot, Dragonite. Charizard, Pidgeot and Dragonite are all references to his anime Pokemon
Professor Elm-Togekiss, Electivire, Magmortar, Jynx evo, Wigglytuff and Clefable. All of these Pokemon are evolutions of what may be from the Odd Egg in the original GS game, with the exception of Pichu(Togepi instead). This links to his research in Pokemon Eggs
Professor Birch-Blaziken, Linoone, Beautifly, Dustox, Mighteyna and Pelipper. These Pokemon are the closest to Litteroot Town, and thus easy for Birch to collect
Professor Rowan-Staraptor, Gliscor, Probopass, Lickilicky, Tangrowth, Yanmega. All but Staraptor are Pokemon that, prior to Gen 4, did not evolve, referencing his study of evolution
Professor Juniper-Cicinnco, Acclegor, Watchog, Klinklang, Musharna, the starter not chosen
Player Character Ethan-Typhlosion, Beedrill, Donphan, shiny Gyarados, Politoed, Sudowoodo
Kris/Lyra/Kotone/Whatever-Meganium, Azumarill, Raticate, Misdreavus, Hitmonchan, Xatu
Player Character Brendan-Swampert, Aggron, Shiftry, Rhyperior, Castform, Milotic
Ethan-Infernape, Clefable, Alakazam, Bastiodon, Lickitung, Rotom
Player Character Dawn-Empoleon, Lopunny, Togekiss, Mamoswine, Pachirizu, Drifblim
Special Pokemon to get in Magma Ruby/Ocean SapphireMirage Island-A mysterious island that's almost as hard to get as before, but its thankfully easier. It is renewed every hour, and the chances of finding it randomly are one in 8192(the same as a shiny). A random number generater goes from zero to 8191. Every hour, you may call the guy in Pacifidlog Town. He will let you enter a number, and tell you if you're lucky. Similar to the lottery, you get consolation prizes-the better the estimate, the better the berry. Chances can increase: if you have a Pokemon of a nature pertaining to defense or special defense, the number generator is halved. If its a Calm nature, its quatered. Its also quatered if you already have a Liechi berry. Beating the Elite 4 results in halving, and filling the Hoenn Pokedex(minus Pokemon #000 and Pokemon #301-302) quaters it even further. Should you have all these, you can have a maximum of 1/64. On the Island there are Wynauts from Lv 5 to Lv 50, with a special shiny Wobbufett guarding the Liechi Berry at Lv 60. Beat/catch and get the Liechi berry, and Pokemon #000 is released. The Mirage Radar(with the old guy talking to you) is used to note the chances, Mirage Island appearing or not, fun trivia asked about rare Pokemon only found in one area(though you have to visit), and finally to locate the mysterious Pokemon #000.
Hidden Ability gifts-Certain trainers, after you beat them, will give you a Lv 5 first-stage of said trainers' main Pokemon. They are:
Roxanne's Sand Force Nosepass, Brawly's Sheer Force Makuhita, Wattson's Minus Electrike, Flannery's Shell Armor Torkoal, Norman's Quick Feet Zigzagoon, Winona's Cloud Nine Swablu, Tate and Liza's Magic Bounce Natu, Wallace's Adaptability Feebas, Sidney's Justified Absol, Phoebe's Prankster Sableye, Glacia's Oblivios Spheal, Drake's Sheer Force Bagon, Steven's Weak Armor Skarmory
Special starters-As mentioned, you can actually catch the three starters of Kanto. After beating the Elite 4, sightings report a mysterious Charmeleon wandering the area. It is Lv 50, catchable(WTF), and with Solar Power. Venusaur and Squirtle have already been mentioned. Once completing the Hoenn Pokedex(with the exception of event legendaries). Depending on the version, you can either pick one of the Johto starters or one of the Sinnoh starters(they do not have their Hidden Ability), given by Professor Birch.
Legendary encounters(main game)-Groudon and Kyogre are found in their respective versions(Lv 45), but to get Rayquaza(Lv 75) you must have both versions. Both are located in the Cave of Origins, filled with either sapphires(Groudon) or rubies(Kyogre) The Sky Tower can be visited prior to the Elite 4, but the Pokemon are still in the level 50s to 60s, so its not advised
With the Regis(Lv 40), I've already described that it involves meeting Brandon. While you must beat him to get the Regis, they will come back after being beaten after a day. Brandon will also help you find their leader Regigigas when you have the three, but its filled with Fighting types and almost as strong as the Sky Tower, with a Lv 70 Regigigas. The Regi chambers, while only having the legendary as the Pokemon, are quite more artistic. Registeel's lair has metal slabs for the walls and a machine sigil where it slumbers. Regirock's lair is an orante cave with stalactites around and stalagmites were Regirock is embedded. Regice's lair is a slippery, frozen region with a glacier containing Regice. All three are buried, and require a ritual to wake up. Regigigas is found in the basement of Sealed Chamber, which you need the Regis to access
With Latias/Latios, they're actually accessed when beating the last gym leader. At Lv 40, it is a roamer. The other is the same South Island event
Then there's mysterious Pokemon number 0. Uniquely, its not only a Pokemon that isn't normally Hoenn, but a Pokemon that you didn't think to find without an event-Mew. 'Course, so much effort to get to Mirage Island makes it worth it. Mew likes to go around the region, though it won't run away from you. The Mirage Radar tells you where to find Pokemon 0, but doesn't tell you what it is. You go into the grass, water or cave, trying to find what it is, and BOOM suprise Mew! When you capture Mew, you get another surprise-the region where Mew was captured will now a wandering Eccentric Ditto there once a day
Legendary encounters(after-game)-If you have Pokemon Magma Ruby, you can try and get the bird trio, and in Pokemon you can try and get the beast trio. Mercifully, they don't roam. You only get Articuno/Raikou at first though. To get Zapdos/Entei requires capturing the previous, and to get Moltres/Suicune you must share keys with the alternate version. All are Lv 60. Articuno is located in the Shoal Cave, Raikou is located in New Mauville, Zapdos and Entei are roamers, Moltres is located at Mt Chimney and Suicune is located in Sootopolis
Lugia and Ho-oh-When the trios are obtained, trade them to other version. Both are Lv 70, and require the trio they master. In Sapphire, the bird trio will unlock Lugia in a deep underwater tornado system, and Ho-oh on a ruined tower