Rayquaza was a post-game event in Ruby and Sapphire, then was featured more prominently in Emerald
Giratina was a post-game event in Diamond and Pearl, then was featured more prominently in Platinum
Kyurem was a post-game event in Black and White, then was featured more prominently in Black 2 and White 2
I'd love to see Pokemon games where the minor legendaries are given more background
Mewtwo, Mew, Lake trio (Although they do help during the main story in DPPt), Legendary Beasts/Birds (Although Suicune was a major part in Crystal and side-quest in HG/SS), Muskateer Trio, and more
Maybe Deoxys will be featured in the Mossdeep Space Center?
and make them catchable in-game...