If you're going clipless, larger pedals will be easier to find with your feet, as well as providing more support under your shoe. This tends to make the pedal heavier, however, and really big platforms tend to be used mostly by gravity riders. At the other end of the spectrum, 'skeleton' mechanism-only clipless pedals are superlight and more-or-less impervious to mud clogging. That said, with very little in the way of support platform or protection, they're best suited to very stiff shoes and more careful riders.
If flat pedals are you're preferred option, bigger is generally better. This is because larger pedals provide a greater surface area for adjusting your feet, while the larger contact area spreads impact forces in drop-offs and jumps. However, increased size can be a catch (literally), as pedals that are too large are more likely to strike rocks and tree stumps as you ride. We recommend trying before you buy – if there's lots of pedal sticking out from under your shoe, try a smaller model.