This is the method I used, but it's not required to use to catch Latios. Stack up on some repels (can be repel/super/or max repel) go to Lilycove City, and head for route 121. Before you hit the grass save, and use one of your repels. I have noticed if Latios is in that area while your using repel, the game will skip while you move through the grass. I knew it had to be Latios because of the continuing skipping. Now as soon as repel weares off Latios should appear.(if game skipped, and from what I see using repel kept me away from Latios, so after it weares away you should see him) If you happen to have used your masterball, and Latios ends up running away, simply reset the game. Note: if Latios does not appear in that area just use Fly, and repeat the method again. Fly will change the area Latios is in, so keep trying. About 1hr later I got my Latios. (make sure you have a pokemon with Shadow Tag ability, or maybe Trap Arena.. such as Trapinch, Golbat, or Wobbufet. Or simple have a move like Mean Look that can prevent pokemon from running.
Good luck finiding him. ~_^
~Blade~
