I'll start.

>Lugia
Female (actually both cuz is a species but it looks more feminine to me)
>Ho-oh
Male (it has a parental aura)
>Suicune
Male (it looks like a femboy)
>Groudon
Male (it looks manly)
>Kyogre
Female (I have always associated water with femininity and it's design looks so majestic and beautiful at the same time that make me unable to see anything masculine on it)
>Rayquaza
Huh... Male (it looks ambiguous to me, but idk maybe I change it later for female)
>Palkia and Dialga
Both male (they look like the fathers of the universe)
>Giratina
Female...? (This looks ambiguos too but it design is a bit feminine and in my headcanon it is the daughter of the nemesis of Arceus. that sounds a bit retarded)
>Reshiram and Zekrom
Female and Male respectively (yin/yang... nothing is white nothing is black each one has a bit of the other that's why Reshiram design is so Feminine and Zekrom design is so Masculine, it's also represented in their eyes: Reshiram has the color of Zekrom thunders and Zekrom has the color of Reshiram flames, and their own games Reshiram in Black and Zekrom in White)
>Zekrom
It's just a empty cocoon.
>Yveltal
Male (represent death and destruction as male qualities)
>Xerneas
Female (represent life and peace as female qualities)
>Lunala and Solgaleo
Dude the pokedex lmao xd

Reminder that:
>All females
Waifufags
>All males
Gays and underages