There are always people that take "Gotta Catch'em All" to heart (myself included) but really that depends on the game. If you are adding every Pokemon into a fan game then it seems strange not to, but if the game has a reasonable region worth of Pokemon somewhere in the range of 250-400 mons, then the games story should really be a driving factor. In the original games the 4 legendary Pokemon where Articuno, Zapdos, Moltres, and Mewtwo. Mewtwo has a back story of being created in a lab to be the worlds strongest Pokemon, but he is viewed just as a really strong pokemon for anyone to catch if you a strong enough trainer and while they don't have a back story the same goes for the birds. Mew was the games mythical Pokemon and while he could only be obtained by glitches or gift events Pokemon Emerald showed us he is out there but is incredibly hard to find if you do not have the Old Sea Chart that will allow you to navigate to Faraway Island where you have to play with Mew to get a chance to battle him.
Sinnoh games on the other hand build up their legendaries to be a group of god-like monsters (even God him self), the 3 sprites that seem to be the personification of humanity, a living nightmare, as well as a hand full of others. To play up the importance of these creatures and their roles to support our world it sorta ruins the story having the player being able to catch them along with leaving plot holes that can't really be filled. Will existence come to an end if you remove the creation trio from their dimensions, if you catch Cresselia without taking care of Darkrai will there no longer be a cure for his bad dreams, If you catch God then does being champion of a region really amount to anything? It doesn't feel right to be able to catch these Pokemon regardless of your title or strength as a trainer.
But that's just my opinion.