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I see this debate happen a lot and I just want to say a few things:
Both are great engines and have their perks.
Both have visually appealing artstyles.
FRLG have a bit more polish with their overworld though, like going slowly down the stairs -- or transitions before going into an area, or the information boxes on the Town Map about landmarks.
Emerald is great, but it's just a polished Ruby/Sapphire -- It doesn't nearly have the same amount of visual and technical ticks that the FRLG engine has.