Wobuffet is a good choice, however it might accidentely KO Latias/Latios with mirror coat. Besides, it's so annoying just to wait and use mirror coat over and over... I'd suggest weakening down, my groudon used slash, then on the second encouter, shock wave (yes, I know, waste of a TM) I got latios down to a sliver of health.
Catch a Lv. 50 something golbat from ruby, or train one up to trap Latios/Latias. Latios/Latias's psychic attacks (especially Latias's) aren't strong enough to do some real damage yet. Keep throwing balls. The Master Ball really helps, because you can just throw it, but you probably used it on Rayquaza to beat the elite 4 fast in emerald (Am I Right?)
Latios/Latias can be most easily tracked if your at maulville city, they appear at 4 routes near there. Use fly if they're located in the ocean, they'll jump somewhere near. But, you'll have to guess if they'll go North, South, East, or West (Hopefully.)