Out of 649 Pokemon, only 47 are Legendary. That's not many.
If you consider evolution families, the figure comes to 14.3% of all families contain legendary Pokémon (47/329). That's a lot.
If it was only the case that legendary Pokémon were
said to have special powers, or even better just be very rare, then that'd be fine. But no, nearly all of them are near godlike and literally have whatever insane powers they're said to have.
The real answer as to why there are so many legendary Pokémon is, of course, because Nintendo then has that many special promos to do with as they please (event Pokémon, make movies out of them, etc.). And they've gotta be special because of that, right? Who wants a boring old non-legendary?
From a realism perspective (which I tend to prefer in a Pokémon world), many more Pokémon would have legends and tales about them (like Shedinja's back hole and tugging on Ninetales' tail), but no Pokémon would literally have such ridiculous abilities as time travel or wish-granting or space-time creation. They would be powerful, certainly, but that's a completely different thing to the godlike abilities Game Freak insist on giving them.
In summary, I can see why Nintendo make so many legendaries, and am fine with it (so long as it doesn't get out of hand), and I just ignore the godlike aspects given to them and treat them as nothing more than rare and powerful animals.
Also gen IV added way too many legendaries. If I'm correct, Hope my counting skills doesn't fail, there are 14 legendaries introduced in ge, IV which is 29,79% of all legendaries are from gen IV. Gen IV added way too many.
Personlly I think they should just add the amount of the 3th gen added with each upcoming gen..
Gens 4 and 5 both have 13 legendaries in them (Phione apparently isn't one). However, Gen 4 only introduced 45 new families of Pokémon (of which 13 were the legendaries; the rest of the Pokémon added were additions to existing families), which is probably why it feels so excessive. In comparison, Gen 5 has over 80 new families, more than even the 70-odd of Gen 1.