While I completely agree that Pokémon sizes are inconsistent through various media, I'm not sure the images you're showing are the best method to view how big or small a Pokémon is. I know that you're very likely referring to general size when mentioning how big the Flying-types are, but still...considering average real-world heights (around 5'4'' for females and 5'9'' for males) and the fact that the character is less than 5' tall, any Pokémon will look much larger next to him in comparison; the Flying-types you listed are indeed much bigger than normal birds, but they aren't taller than most people over the age of, say, 12.
I think one of the biggest offenders of the size discrepancy is Roselia. From what I've read (haven't watched the anime since the start of the Orange Islands), Drew's Roselia comes up to his waist...quite an impressive feat for a Pokémon whose average size is a mere 1'0'' in the games.