Pokemon Indigo (Gen 1(and technically 2) sequel)
Legendary birds-Like before, the legendary birds are available, but with a twist. Before you go on Victory Road, you must prove one last challenge by catching them. They have an increased catch rate of 45, however there is a totem Pokemon guarding them. They are Level 50
* Articuno is found in the formerly blocked off area of Seafoam Island, in the "Seafoam Peak" region. Its totem guardian is a Lapras, who summons Slowbro and Cloyster.
* Zapdos is found on the top of the Kanto Power Plant Tower, now accessible. Its totem guardian is an Electivire, who summons Magnezone and Electrode
* Moltres is found on Mt Ember. Its totem guardian is an Arcanine, who summons a Machamp and Golem
Mew-Mew is actually the main legendary boss, having judged you worthy of confronting it. After beating the champion, you may catch it at Level 60.
Mewtwo-Mewtwo is achieved after defeating Johto and becoming champion a second time. It has returned to dwell on the top of what used to be Cinnabar Island, which functions as the Unknown Dungeon now. Depending on your gender, it will already hold a Mewtwonite X or Mewtwonite Y and Mega Evolve in battle. It is Level 80 and will only appear if you have a Mew in party. It has created a home for it, the "Unknown Lab"
Legendary beasts-If you successfully managed to capture Ho-oh and have it in your party, you are able to evolve your Vaporeon, Flareon and Jolteon into Suicune, Entei or Raikou. However this is a very special ritual and you can only achieve this evolution once, so be careful. They explain the original legendary beasts were born when Ho-oh revived them in more powerful forms
Musketeer quartet-Replacing the beasts as roamers are the musketeer quartet. After getting the first three, you are able to finally catch Keldeo in-game so long as you have the other on your team
Lugia and Ho-oh-Achievable on Navel Rock, which is only available with the legendary birds and beasts caught and the Champion defeated twice. They are Level 75
Celebi-A QR Code event. You are capable of using the QR code to unlock the GS Ball key item, summoning Celebi
Latias or Latios-Pokemon you can find on the Sevii Islands. Which you get depends on gender, however as mentioned there is a ritual to get the other one
Pokemon Spear(Arceus centric DPPt sequel)
Weather trio-The last bosses after-game, at Level 70 and then Level 80
Darkrai and Cresselia-Darkrai is no longer an exclusive to events. In Canalave City to solve the boy's nightmares you do not try to find the Lunar Item, but go to the source. However its not enough due to the kid already suffering from bad dreams before Darkrai, and you need to catch Darkrai to prevent the effects from lingering
Phione and Manaphy-Uniquely Phione can be found as an ultra-rare fishing Pokemon almost anywhere in sea. However a one time item is capable of evolving them into Manaphy, the Sea Crown
Regigigas-In Snowpoint City Regigigas causes trouble. After stopping the rampage, you can use it post-game to create one of each of the Regi trio for you
Arceus-The main Pokemon of the game, and target of the empowered Cyrus
Creation trio-After catching Arceus you can go after these. It is explained as Arceus creating a new Creation Trio due to the current one being taken out of comission and as so to keep the fabric of space-time safer
Lake trio-After catching Arceus you can go after these
Shaymin-A QR Code, allowing you to get it in Floroama Town
Pokemon Stars and Prism(Sun and Moon sequel)
Tao trio-A former Team Plasma agent earlier on reveals that he has been trying to created the original dragon through Kyurem's DNA, under orders from Ghetsis as a back-up. However it took too long for him. You first get a Level 5 Kyurem, however the other Tao Pokemon flees. Later on you can catch that one at Level 70, and in Stars its Reshiram while in Prism its Zekrom
Xerneas and Yveltal-These are explained as being the member of the mortality duo that you didn't get in Y or X. They traversed to Alola because they felt needed.
Zygarde-Zygarde returns with more detail. Under Route 16 is a discovered "Zygarde Nursery". It is revealed that if Zygarde is to be incapacitated, the Nursery will begin producing more Zygarde. The process has been accelerated due to the appearance of Ultra Beasts. You are given one Core and 20 Cells for certain achievements. First achievement is getting there with a box of five heart affection in Pokemon Amie, showing your worthiness in being a trainer. Second is to train six Pokemon on your team to Level 45. Third is to complete the Elite 4. Four is to successfully capture a Xerneas or Yveltal. However there are initially 20 Cells and 1 Core out in the wild
Shiny Guardian Deities-Something that is event only. These are triggered by an event, causing it to reveal that alternate universe versions of the Guardian Deities failed in protecting their Alola from the Ultra Beasts and fell into this reality. They have a movesets they normally can't get, and initially have their Hidden Ability. However the Tapu Key can switch their ability
Necrozma-This is the main legendary, having two more powerful forms; Solar and Lunar. Both are Psychic/Dragon with expert defense. However their other stats have a really different distribution, and different abilities
Cosmog-Because of the dimensional anomalies, two Cosmog end up falling out of interdimensional space after facing Necrozma. They will become Solgaleo in Stars and Lunala in Prism