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twintail said:
because nintendo seem to do it on a consistent basis.

That has probably some thing to do with the fact that most of these  fangames are games from the 8/16 bit era, where Nintendo reigned supreme and had the most recognizable IPs these days.

Sega for instance killed remakes of Bare Knuckles (Streets of Rage) shortly after supporting the developers, probably for the same reason that Nintendo does it: It's lawyers told them that they need to protect their IP, as IP laws make no distinction between copying an IP for profit or as an hommage.