In the games you can also catch God and creator of the universe and use it to smack around Magikarp.
In other words, you shouldn't really use the games to explain away any unrealistic ideas. Take a look at the anime or the Special manga to see where others get their ideas how legendaries should be handled. I know that in the anime, if you catch a legendary, the world nearly ends. The games have a little trouble of not being realistic. That was one of the jokes about HG/SS, where the player could wander around with Arceus and no one cares.
But in fanfiction, you want to aim for realism the best that you can. If your character is wandering around with one or two or three Pokemon told about only in legends, people should seriously react.
I don't think this was worthy of another post, but I think this could help as well and it only reinforces Astinus's point. In a fan fiction I wrote a few months ago (that i didn't post) I was going to have a couple of scientists search for legendary pokemon eggs. Then I struck a problem. Legendary pokemon don't have a gender! I'm not too sure about a genderless Pokemon, but I'm pretty sure the game developers made it that way so people wouldn't breed hoards of legends. For instance I find it incredibly difficult to believe Lugia have no gender in the GAME because in the ANIME Team Rocket tries to steal a baby Lugia away from its mother.
In real life there is no such thing as a genderless living thing unless it's microscopic life or some marine organisms. Things start getting complicated because we get into stuff that replicates itself to breed, such as cells.