My idea for the second mascot hinges on the inclusion of Johto. If the sequels stick to just Kanto, then I don't even think there's a good reason to wait until 2018.
So here it is: A corrupted Celebi form to serve as Mewtwo's counterpart. While Mewtwo is a separate species from Mew, it is actually quite comparable to Hoopa Unbound. And since Celebi is Mew's counterpart, a bigger and darker form would be Mewtwo's counterpart. And that form would solve the GS Ball mystery.
I am not sure you know this, but the GS Ball in Crystal didn't actually contain Celebi. Basically, the ball started to shake as Kurt was examining it, and even Ilex Forest itself became restless. When the player inserted the ball into the shrine, Celebi descended from the sky, implying that it wasn't already in the ball. So what was? I used to speculate for years that it was an undiscovered legendary, but what if it turned out to be a Celebi from another era or even timeline?
There is another interesting fact about the GS Ball distribution: It was unlocked by a feature called the News Machine in the Goldenrod Pokémon Communication Center. There was a nice story to this: A person called Chieko contacted the player through the News Machine. There were three requirements to obtain the GS Ball: First the player had to win against Chieko in a mini-game, but after doing that, Chieko would interrupt the communication by telling the player that they had to collect all 16 badges. Once the player had all badges, they could resume the communication, prompting Chieko to ask them a list of yes/no questions in order to test their "heart as a Pokémon trainer". I had someone translate the questions years ago:
1) Should Pokémon protect people that aren't their trainers? [Yes]
2) If a Pokémon is afraid of a person, is it the person's fault? [Yes]
3) Should a person who loves Pokémon strive for a goal other than being a trainer? [Yes]
4) Is a child a weaker trainer than an adult is? [No]
5) Do you think that the legends from the days of old are all a lie? [No]
If the player answered all five questions correctly, Chieko would recognize them as "a splendid trainer with a strong and pure heart" and tell them they were worthy of the GS Ball. The communication would end, but only upon leaving the center would a nurse approach the player to give them the GS Ball (that part was actually localized, but never used).
I've saved the real twist for last. The title of Chieko's activity in the News Machine was "a gift that transcends time", obviously in reference to the GS Ball. This implies that the GS Ball came from another time. The future or the past? What about Chieko herself? She curiously described herself as an Apricorn Maker from Azalea Town. Kurt is the only Apricorn Maker in Azalea, or anywhere in the games for that matter. If that alone doesn't make it obvious that Chieko herself communicated with the player from another time, then this does: In the anime, Kurt's grandaughter is called Chie (Maisy in the dub). Even though her name wasn't revealed in the games, it is safe to say that Game Freak gave her the name, and intended for Chieko to be her adult counterpart. It is hardly surprising that Chie would want to follow her grandfather's footsteps.
So here it is: A corrupted Celebi form to serve as Mewtwo's counterpart. While Mewtwo is a separate species from Mew, it is actually quite comparable to Hoopa Unbound. And since Celebi is Mew's counterpart, a bigger and darker form would be Mewtwo's counterpart. And that form would solve the GS Ball mystery.
I am not sure you know this, but the GS Ball in Crystal didn't actually contain Celebi. Basically, the ball started to shake as Kurt was examining it, and even Ilex Forest itself became restless. When the player inserted the ball into the shrine, Celebi descended from the sky, implying that it wasn't already in the ball. So what was? I used to speculate for years that it was an undiscovered legendary, but what if it turned out to be a Celebi from another era or even timeline?
There is another interesting fact about the GS Ball distribution: It was unlocked by a feature called the News Machine in the Goldenrod Pokémon Communication Center. There was a nice story to this: A person called Chieko contacted the player through the News Machine. There were three requirements to obtain the GS Ball: First the player had to win against Chieko in a mini-game, but after doing that, Chieko would interrupt the communication by telling the player that they had to collect all 16 badges. Once the player had all badges, they could resume the communication, prompting Chieko to ask them a list of yes/no questions in order to test their "heart as a Pokémon trainer". I had someone translate the questions years ago:
1) Should Pokémon protect people that aren't their trainers? [Yes]
2) If a Pokémon is afraid of a person, is it the person's fault? [Yes]
3) Should a person who loves Pokémon strive for a goal other than being a trainer? [Yes]
4) Is a child a weaker trainer than an adult is? [No]
5) Do you think that the legends from the days of old are all a lie? [No]
If the player answered all five questions correctly, Chieko would recognize them as "a splendid trainer with a strong and pure heart" and tell them they were worthy of the GS Ball. The communication would end, but only upon leaving the center would a nurse approach the player to give them the GS Ball (that part was actually localized, but never used).
I've saved the real twist for last. The title of Chieko's activity in the News Machine was "a gift that transcends time", obviously in reference to the GS Ball. This implies that the GS Ball came from another time. The future or the past? What about Chieko herself? She curiously described herself as an Apricorn Maker from Azalea Town. Kurt is the only Apricorn Maker in Azalea, or anywhere in the games for that matter. If that alone doesn't make it obvious that Chieko herself communicated with the player from another time, then this does: In the anime, Kurt's grandaughter is called Chie (Maisy in the dub). Even though her name wasn't revealed in the games, it is safe to say that Game Freak gave her the name, and intended for Chieko to be her adult counterpart. It is hardly surprising that Chie would want to follow her grandfather's footsteps.
If they approached it as you've described, then I do think the plague plot could work in Kanto. You certainly seem to have thought it through, and I think that's key to making a good story.
I'd also say we're already somewhat into fanfic territory here. Though it's not as if some of the *actual* games' stuff doesn't read like fanfic when written out (and not even very inspired fanfic, at that), and lord knows I've made my share of those sorts of comments. I'm interested in what you have to suggest, since as I said, you do seem to have put a lot of thought into the idea of Kanto sequels.