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The following headcanon ignores my previous timeline calculations in favor of more accurate theories posited by others.
The armor Giovanni forced Mewtwo to wear not only suppressed/focused its powers, but also monitored/analyzed its physiological makeup and capabilities, essentially reverse-engineering it and creating a backup "blueprint", if you will (assuming that the original data collected by Dr. Fuji's group was lost). MechaMew2 (from Pokémon Live!) was partially based on this blueprint, and was already in the pipeline as a contingency plan prior to Mewtwo's escape. This explains how Giovanni could already have it built and tested just three or four months after the events of Mewtwo Strikes Back (assuming Pokémon Live! is intended to take place directly between Adventures in the Orange Islands and The Johto Journeys).
(As an aside, discrepancies between The Birth of Mewtwo and Pokémon Live! can be resolved by merely reinterpreting some of Delia's dialogue as a distortion of the truth. Although she makes it sound like she simply fell in with a group of juvenile delinquents—implying that she and Giovanni are close in age—it's more likely she didn't want to admit that she was a full-on member of Team Rocket who was manipulated by a much older man. Her statement that Giovanni founded Team Rocket later on, as opposed to inheriting leadership from his mother, could be taken to mean that he significantly restructured the existing organization to the point that it was almost entirely remade from the ground up.)
During the events of Mewtwo Returns—taking place at the end of that same year—Giovanni attempted to recapture the existing Mewtwo rather than making a second one. There were several reasons for this—chief among them, simply creating Mewtwo after Mewtwo until one of them finally obeyed would not only be prohibitively time-consuming and expensive, but the sheer number of rejects would surely pose an unimaginable threat to Team Rocket—and, indeed, the entire world.
Although Team Rocket's memories of Mewtwo were ultimately erased, the data they had collected previously was not lost. Under unknown circumstances, it was rediscovered sometime later, either by eventual defectors from Team Rocket or a group of complete outsiders. This enabled the creation of a second Mewtwo four years later, paving the way for Genesect and the Legend Awakened.
The armor Giovanni forced Mewtwo to wear not only suppressed/focused its powers, but also monitored/analyzed its physiological makeup and capabilities, essentially reverse-engineering it and creating a backup "blueprint", if you will (assuming that the original data collected by Dr. Fuji's group was lost). MechaMew2 (from Pokémon Live!) was partially based on this blueprint, and was already in the pipeline as a contingency plan prior to Mewtwo's escape. This explains how Giovanni could already have it built and tested just three or four months after the events of Mewtwo Strikes Back (assuming Pokémon Live! is intended to take place directly between Adventures in the Orange Islands and The Johto Journeys).
(As an aside, discrepancies between The Birth of Mewtwo and Pokémon Live! can be resolved by merely reinterpreting some of Delia's dialogue as a distortion of the truth. Although she makes it sound like she simply fell in with a group of juvenile delinquents—implying that she and Giovanni are close in age—it's more likely she didn't want to admit that she was a full-on member of Team Rocket who was manipulated by a much older man. Her statement that Giovanni founded Team Rocket later on, as opposed to inheriting leadership from his mother, could be taken to mean that he significantly restructured the existing organization to the point that it was almost entirely remade from the ground up.)
During the events of Mewtwo Returns—taking place at the end of that same year—Giovanni attempted to recapture the existing Mewtwo rather than making a second one. There were several reasons for this—chief among them, simply creating Mewtwo after Mewtwo until one of them finally obeyed would not only be prohibitively time-consuming and expensive, but the sheer number of rejects would surely pose an unimaginable threat to Team Rocket—and, indeed, the entire world.
Although Team Rocket's memories of Mewtwo were ultimately erased, the data they had collected previously was not lost. Under unknown circumstances, it was rediscovered sometime later, either by eventual defectors from Team Rocket or a group of complete outsiders. This enabled the creation of a second Mewtwo four years later, paving the way for Genesect and the Legend Awakened.
