I've been having this same thought lately, about the scales of time that exist below/inside what we perceive. I agree that smaller/simpler brains probably run on a higher clock speed than those that are larger or more complex, and that impacts perception. But even within the fastest little minds, the rate at which chemical reactions take place or electrical signals propagate make them seem glacially slow in comparison.

I was actually thinking about putting a little video together about these scales of time, with the video containing nothing more than a person's blink reaction slowed down 5,000x.