I don't quite agree that there were to many, though it could have been handled better.
Regigigas felt necessary as a legendary, because they did not have a leader, and without a leader their threat wouldn't have really mattered to the point of being sealed away. Plus they felt like keys to a greater force, which Regigigas embodies.
The lake spirits were the sprites of the reigon, giving the player a smaller, more trickster-like Pokemon to seek, rather than the gods like Palkia. Plus they embodied the forces of man, emotion knowledge willpower, which had no origin beforehand without the assumption that they're exactly like us.
Heatran was very cool, but felt very black sheep in comparison. He wasn't connected to the main story, so you had no true motivation in game to go find him beyond the volcano erupting.
Creslia and Darkrai were very cool legendaries, but I never understood why one was event only, while the other was a (very annoying) roaming pokemon. They also lacked true motivation within the main story line.
Manaphy, Shaymin and Arceus I can't really comment on, since all being event only, it would be impossible to make them very important in the story, but also prevent anyone from getting them within the game. It would feel very broken.
All in all, its not that the legendaries were to many in number, but that only a few of them made appearances within the story line, and thus get the player to make them feel the foreboding sense of them and their power. So I will say their were to many event exclusive Pokemon, but that's a different concept than just having to many legendaries.
