Came across an interesting glitch with this one (at least, I think it's a glitch). I had the master code, wild shiny pokemon, and male adamant nature codes on, and captured a Taillow. I then noticed I was having some difficulties with my starter, as in it was ignoring my commands. I thought the game had just managed screw itself up somehow, but when I checked the IDs, I found that my ID had changed to 00000, like Taillow's, while Treeko's was 04400.
Again, not sure if this is supposed to happen, just found it interesting. Also, fighting Roxanne is gonna suck.