I'd want to see the 'fic before I make any judgements about it, but even if you are working with an overused plot, there's nothing wrong with trying--it's important to practice to improve as a writer. I say, go for it, and if it doesn't turn out that great you can improve it. What's more important is that you're writing a story that you enjoy; having others like it is kind of a nice extra.
Using legendaries depends on how you depict them in your story; I see that you're going to go with the view that they're just like any other pokémon, but rare and more powerful. That can work, but necessarily your villain's intimidating factor will go down for the other characters in your story, since he's done something hard, yes, but not incredible (i.e. caught an anime-style 'god' of [element]). Which isn't to say that it's not worth it, it would still be impressive (to the other characters) if he had a team of them, when the very best trainers would normally only have the time and effort to devote to catching one.
Personally, I feel that legendaries 'giving' themselves to trainers, even temporarily, is more unrealistic (and trite, as we've seen it so many times in the anime) than a trainer managing to catch one via luck and strength and guile. I myself prefer, "I have this pokémon because I was strong enough to defeat and capture it", to "lolz teh legedns liek me cuz Im suhc a kewlies persun adn coem adn help me wehn itz convenent 2 teh plot!!!1"
I feel that it's very important that the trainer pay some sort of 'price' when capturing a legendary--it should change them as a person. They should spend years tracking the thing down, training their pokémon so that they'll have a chance against the legendary, researching--almost obsessive behavior that will strain their social relationships. The only good legendary-capturing 'fic I ever read was about a trainer whose expedition team-member died in the process, and who nearly died himself--first in the process of capturing the legendary, and second when the government caught up with him.
I did read another 'fic where the legendary capture wasn't the -focus-... it was Clouded Sky, by Negrek. Anyway, that one was good because the girl caught an injured Raikou--and the portrayal was realistic because all it did was try to run any time that she let it out, and eventually had to bring it to Professor Elm because she couldn't handle it. Which brings up the question of, how will your villain control his legendaries? I'll leave that up to you, but there are many ways it could be achieved.
'Journey' 'fics are fine, as long as you spice them up from the base level of "[character] walks around and gets badges, ho-hum." With villains it's hard to win, because you either get "blah, Team Rocket again?" or "new threats are soooo lame!" In my opinion, the best thing you can do is not to worry about it, and just concentrate on making the villain(s) as good as possible: they should be worthy adversaries, not saturday-morning cartoon-stock bumbling henchmen and the like.
Klaus said:
Now,for the legendary thing, in realistic terms, a legenday could rip, tear and any other mutilation you can think of, a human.
True, but so could almost any other pokémon, not to mention inflict various types of elemental damage. I think a wild pokémon being able or intending to hurt a trainer would be something the trainer -expects-, not something to deter capture unless you're going to limit yourself to Lv. 5 Igglybuff and Cleffa.
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