Here is the answer.
That is how GameFreak wanted it.
That is how GameFreak wanted it.
That is how GameFreak wanted it.
That is how GameFreak wanted it.
That is how GameFreak wanted it.
But in regards to your Zekrom / Reshiram having a higher catch rate, there is definitely a good reason. Remember, in the original Black and White, before you fought N, you were forced into battle with Zekrom / Reshiram. It would keep attacking until you caught it / ran out of Pokeballs. It is quite likely that Game Freak preferred you to catch the dragon right there (to help against N), which is why it has the higher catch rate.