Boy, do I gotta keep using this anology? Think in terms of Superman/Clark Kent. No one but us viewers can see that Clark Kent is Superman with glasses on. It's hard for the people in the show to tell it's them, while it's made blatantly obvious for us.
Remember, Satoshi is the MAIN CHARACTER of the show. That alone makes him special. It'd be boring to not show any of the Legendary Pok?mon. o_o But do remember that he's not the only one that's seen 'em. We have Todd who spotted Articuno, a child that's befriended a baby Lugia before Satoshi ever met one, Euisune has seen Suicune and Raikou, Kenta/Marina/Jun'ichi all met Raikou as well, two standard Johto filler characters met Entei and Zapdos..
Spoilers AHOY!
Team Magma got a hold of Kyogre and Team Aqua got a hold of Groudon much before Satoshi-tachi caught a glimpse of them.
So Satoshi isn't the ONLY one who meets 'em. Hell, even Masato developed a bond with Jirachi whereas the others didn't.