It's because the blue slime was the first and weakest enemy in Dragon Quest 1, which was the first video game RPG. Every time you see a slime as the lowest monster, that is a homage to Dragon Quest.
This is especially true of Japanese games. In Japan, Dragon Quest is huge. When a new Dragon Quest game comes out, employers give people the day off because they know employees will lay out to go buy the game. It's like Halo 3 in the US, but even bigger.
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