Transperant gives more depth. And gives you the ability to work in layers. (everything you've done in the previous layers remains visible and gets darker with each layer)
With opaque colors the color does not get darker with each layer but stops at the color you see in the bottle.
That's the difference in short.
Which set? Indicate how much you want to spend. Illustration Colors Primary Set 5088-01 is the cheapest.
But for a better start, I recommend the Illustration Color Wheel Set 5080-01.