Do NOT use your masterball on Groudon/Kyogre.
Better saved using it on Latios/Latias or Rayquaza when you get to him.
Paralyze does make catching easier, just throw a few more ball's, i have bad luck catching pokemon, but i managed to catch Groudon, and the 3 Regi's without using masterball, just took some time.
If you breed Plusle and Minum, whichever one was the mother is what the baby will be. To get a pichu, you need to breed a female pikachu (found in safari zone) with either a Male pikachu, or some other compatible pokemon (i think)
You get a master ball in the team magma/aqua hideout, and if you have *all* digits correct in the lotto, you can also get one there.