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I agree that there are too many legendaries per generation in the last few generations.
Five from gen I
Six in gen II
Ten in gen III
Fourteen in gen IV
Thirteen in gen V
Anything over 10 per region in my opinion is too much but generally I wouldn't mind.
Lets look at Gen IV (Shinnoh), where the legendaries that relate to the main storyline are Arceus, Dialga, Palkia, Giratina, Uxie, Mespirit and Azelf. That's a decent amount of legendaries right there but on top there's Regigigas (exception I know), Cresselia, Manaphy, Phione, Shaymin, Heatran and Darkrai. I am completely okay with "side mission" legendaries but having 7 of them in one game feels like overkill.