Why pokéballs?

[Phyresis]

Because the creators lacked the balls to do anything else. (Pun totally intended.)

[TheGreatErenan]

To allow for "that's what she said" jokes.

[TheUberKid]

Yeah! They just had to waste tons of money and effort to shape them into prefect spheres. Makes perfect sense!

[Setorines]

Well odds are the pokeball was created before the Pokemon. If evolution teaches us anything it's that humans would never survive in an environment where the animals can breath fire, or shoot water, etc. meaning Pokemon were a science experiment.

To add to this when surge is meet there is a mention of a great Pokemon war recently which goes to show that these creatures of science were created with the intensions of war as are most great inventions.

Now with this said it seems logical that the way to control these creatures would also have a method of release that allows for a moderate distance and quick reaction times. ie. a sphere.

[TheUberKid]

Well, according to a legend from a pokemon movie, Pokemon existed before Pokeballs. They were used as slaves, and were called "magical creatures".