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The leaked source code for Ruby and Sapphire shows that Emerald was planned as early as 2002. The file shown in this image, src_jp_final/source/version.h, has a last modified date of October 8th, 2002, 5:21 PM EST.
Interestingly, it seems that FireRed and LeafGreen were not planned during this time, as VERSION_RED and VERSION_GREEN are nowhere to be found in the source code for Ruby and Sapphire.
VERSION_EMERALD is also mentioned in src_jp_final/source/p_status.c.