I can only think of a few

I can only think of a few.

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Gordon Freeman

Zidane

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Tom Clancy

Serge from Chrono Cross uses a double-ended polearm that the game calls a "swallow".

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Suikoden 2 MC uses tonfa. 1 uses a staff. I think the other suikoden games MCs used non sword/fist stuff too.

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Yuna in FFX-2 and FFX if you count her as the protagonist, which you should.

In Cybersleuth your main weapon is Digimon.

thief swords are still swords

Arc from terraningma uses staves and spears

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