Which one is natural? Or what would you say?
Time goes faster than you think. and Time goes quicker than you think.
It goes faster than you think. and It goes quicker than you think.

Question

Which one is natural? Or what would you say?
Time goes faster than you think. and Time goes quicker than you think.
It goes faster than you think. and  It goes quicker than you think.

Answer

Good job!  All are fine. Here are a few additional ways you could say it 
Time moves quicker than you might think.
Time marches more rapidly than you realize. 
Time vapes in the blink of an eye. 
Time unrelentingly advances.

Answer

Time passes faster than you expect - would be my preference.

Answer

They're all OK, but I'd suggest adding 'by'  e.g. Time goes by faster than you think.

Answer

Both make perfect sense. In my opinion it would flow better if you replaced "goes" with "moves."