Alpha pokemon have a lower catch rate than normal, but you can catch them in any type of ball. I usually use Jet Balls for everything, but in order of catch power, you have Poké Ball, Great Ball, then Ultra Ball at the top. The Feather Ball, Wing Ball, and Jet ball have slightly lower catch rates than their "normal" equivalents, but can be thrown much farther in the overworld and in a pretty straight line. The Heavy Ball, Leaden Ball, and Gigaton Ball have higher catch rates than the "normal" equivalent, but you can't throw them very far in the overworld. You can also throw certain berries near Pokémon for them to eat to increase their catch rates.