It really does depend on what you consider "legitimate" honestly. Some people will shrug and tell you it's fine as long as the Pokemon could be obtained in the game - i.e. they don't have impossible stats or movesets - and you're only doing it on your own personal save. Other people will want to string you up by your ankles and light a bonfire under your head. If you're OK with using Powersaves, there's absolutely nothing to say that you can't do this or that what you're doing is morally objectionable: your game, your rules, your standards.
Personally, I think it's fine - there's nothing wrong with it, because Game Freak have orchestrated this so that it's impossible to do by yourself unless you were lucky enough to catch the event-only Legendaries the first time around and are prepared to buy multiple consoles and multiple games. As long as you keep the Pokemon within the realms of possibility (i.e. don't give a Bulbasaur Flamethrower) there's no reason why you shouldn't fill in the gaps you can't fill in otherwise, or as many as you would like to. Play as your conscience dictates and how you will gain the most enjoyment, and not how other people tell you the game should be played.
