One thing I never understood is why the commandos in RE4 (in the last chapters) didn't use guns, but medieval weapons, like crossbows, axes, flails etc. Some even wear weird armor like this.

There are a few commandos that use gatling guns, so we know they are able to use guns. There are also a few that use rocket launchers. Since the island is the commando's base, there should be plenty of guns around. I always wondered why they don't use guns... it looks so stupid.

Could it just be Capcom's laziness or is there another reason behind it?

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I think part of it is capcom wanted to give the impression these people were pretty behind the times, which is why they were so easily fooled into believing a bogus ritualistic religion. But like you said, there's dudes with gatling guns and rocket launchers soooooo... I have no idea. As much as I love RE, it's definitely got it's WTF moments. Good call on the gun thing though.