Latios pokeball over throw tendency very high?

So far, yes. But it should improve after we get accustomed to its moves and distance.

I find this to be the easiest Legendary to hit, so far. And I finally pulled off the set circle trick. Thanks ProdigiesNation!

It suffers from the same bug that all pokemon that move up and down do:

If you throw at it while it is up high, then even after it comes down the game continues to aim your throws at the higher position.

Either only throw while it is in the lower position, or after you forget and throw at the upper position only throw at the upper position.