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Alright I'll bite
Look the case with Gen 1 legendary Pokemon and Gen 2 is that they didn't have a fancy setup they were eluded too by Npc's and other plot devices and they were not central to the game's development.
They're strong and a hallmark of their games as not necessary to beat or interact with to beat the main quest, but something you get to complete the pokedex or can help you along the way.
the main plot point after these generations becomes the evil team attempting to harness the power of a legendary and it is shoved in your face for much of the main quest.
There is no mystery to them, because all though they're legend they'll make their debut in a all or nothing battle against the PC in a scripted event, which as a plot point I'd say only Platinum did it right. (Despite the fact Giratina is on the goddamn box I still consider his appearance to be the best of any legend)
The next thing we come to are the 'Mirage Legends' and another thing that kills the meaning of being a legendary pokemon, Mew, Celebi, Shaymin, manaphy all of these are Mirages you can hear of them and see them in other media but you cannot get them without Nintendo or a cheating devices intervention.
Which has and always will be BS, it honestly to me would make more sense to flip over a truck to find a mew playing hide and seek and flying across the region hiding than have to go to nintendo world to download it.
TL;DR Downloading and constant reminder of legendary Pokemon kills the mystery and discovery aspect of the game.