I do think it would be cool if TMNT took place in other locations.
Somewhere on the Californian coast might be interesting. Especially since California is a hellova lot closer to Japan than New York. And having the turtles living near a beach might be a huge convenience to them.
And boy, if Mike HAS to have a surfer attitude, it's much more appropriate there
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The San Francisco Bay area would be a pretty interesting location.
It has the fourth largest Japanese-American population in the US, it has beaches for the turtles to use to their advantage, it has Silicon Valley where TCRI and Stockgen could be stationed...I think there's a lot more there that would make more sense story-wise than in New York.
Plus, it would be so much warmer year-round unless they have to go into the mountains in northern California at some point.