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Iwata unironically saved gen 2.
Initially, the urban legend was that Iwata helped with fitting Kanto in. His help was further solidified with GF reference him in HeartGold and SoulSilver.
However, internet midwits pulled an "ackshually" and commented on the fact that the compression is not actually optimized for space but for speed and GF was likely going to have Kanto in no matter what, and it was already a gutted version of it to begin with.
HOWEVER, Nintendo's influence over GameFreak cannot be understated due to the nature of it's Japanese inter-relations via Creatures and Hal, which are in essence still just Nintendo with extra steps. It is incredibly likely and almost the obvious reality to anyone living in Japan at the time that Iwata's contributions are probably much, much, great than even just compression speed.
If the development of Gen 1 is anything to go off of, it is completely within the realm of possibility that GameFreak was STILL shit at programming and that Iwata, a recognized powerhouse at everything he does, DID in fact save the development of Gen 2.