Throwing after the attack animation decreases capture rate
So my capture rate is around 40 percent for legendarys, with very high numbers of Articuno and Zapdos catches, but awfully low on Lugia and Moltres (the only one I actually want badly).
I get a good number of balls, usually 9 - 11 and I hit say 7-9 of them, with curve, mostly Golden Razz, mostly nice or excellent throw.
Lots of the legendaries flee though. And the only thing I do differently than others is throw when the bird is down and after the attack animation.
But I only caught Lugia when I threw the ball when Lugia was at the top and with a super large inner circle.
So to me it seems like hitting after the attack animation seems to be a bad idea.
Answers
you have to take Lugia seperate.
Lugias Catch Rate is much lower than the other birds
I have 7/8 on Articuno 9/12 Moltres and 5/8 on Zapdos.
Which is little above average i think with about 10 Balls in average.
And then theres Lugia i have 1/4.
And its no surprise it´s so low because with fewer balls chance of catching Lugia is ridicoulisly low.
Just hit all balls and if possible grat or excelent and your good to go.
The rest is just RNG and Luck (critical catches i got 3)