Why isn't Lugia a water type?
Well you see. Lugia didn't always live in the water and was the 'diving' Pokemon.
If you remember he lived in the Brass Tower before he lived around the Whirlpool Islands. When the tower got burned down he had to leave.
I assume, he got caught on fire and had to dive into the waters around the Whirlpool Islands. This is why he lives there and why heis not as feathery as Ho-oh.
As for him being Psychic, I believe it is suppose to represent the mind while Ho-Oh's Fire is suppose to represent the spirit. So they were the birds of mind and spirit.
However, after the fire they took on new identities. Ho-oh represented unite and Lugia represented solitarily.
Or, that's what I think at least.
Why isn't Salamence called Flygon?
Because Bagon's and Shelgon's japanese names don't end with gon. Flygon's, however, does.
Why isn't Gyarados a dragon type?
I'm only going to say this once.
BECAUSE YOU CAN FIND THEM FREAKIN EVERYWHERE YOU IDIOT!!!!! IT WOULD BE WAAAAAY TOO EASY TO GET A DRAGON TYPE!!!!!1+SHIFT!!! AND WE CAN'T MAKE THEM RARER BECAUSE THAT WOULD DEFEAT THE PURPOSE OF MAGIKARP!!!!!!!!!
That's is all.
Why aren't Psyduck and Golduck psychic types?
That's a very good question.
It's mostly likely due to the fact the psychic type was one of the most powerful types at the time making psychic types harder to catch.
So, they decided to make it a little bit easier for players by giving them a Pokemon that wasn't psychic but could at least use psychic moves.