Yeah he flies away the first time when your trying to calm Kyougre and Groudon.
(If you go back for him SAVE before walking into him)
Only lazy people and trainers with no skill use Legendaries for the E4 (IMO), on my Emerald rom I caught Kyougre, Groudon and Rayquaza along with the Regi trio, I only went Legendary hunting after E4 though but I don't usually touch Legendaries as they are like Trophies for me.
Sure some of them are good pokemon but yeah, I like knowing just I caught them and that's it.