Godzilla as a mind-warping alien presence akin to Lovecraft's great old ones would be an interesting take. Unfortunately, I don't think even that could make Godzilla scary for me, after all the cheesy rubber-suit movies I've seen him in.
It's sort of the same way that He-Man's nemesis Skeletor took the whole "having a skull for a head" thing, which ought to be terrifying, and managed to make it completely ridiculous. So much so that whenever I see any skull-faced villain now, my first reaction is "Ha ha, he looks like Skeletor."