Why would they put such a random(but noticeable) thing into a game? In case they didnt know, genders are meant for reproduction and you should not have a gender if you cant reproduce, unless they are just completely infertile. Why do you all think they have genders?
The same happened with the Lati twins.
To me, it's just another small difference they put in that just further proves that there's no real "rule/requirement" to be a legendary Pokemon. Or if there is, Gamefreak can easily change it.
Gen I: Legends are one-off Pokemon (or not at all, as far as Mew was concerned, initially); not connected to the plot except in vague ways; genderless; single type; part of some "family" of Pokemon (bird trio, Mew-Mewtwo)
Gen II: Celebi introduced not being connected to any other of the legends and also introduced obtaining by key item. Direct relation to plot.
Gen III: Introduces different genders (Lati) and a Pokemon that has never had an in-game location (Jirachi). Kyogre and company continued being connected with the plot.
Gen 4: Another gender legend (Heatran), 2 legendary Pokemon that can breed (Manaphy w/ ditto=Phione, Phione with Ditto=phione) and one legend that can get multiple copies of in the same game (Phione).