Pr sure in Emerald you can't even catch any of them except Rayquaza until post-E4, so it's not like you'll have the choice til later.
It seems like you have your flying and surfing/diving HM slaves covered, so I'd suggest just adding in other types of Pokemon or perhaps more water types since water types are overpowered and there's TOO MUCH WATER in Hoenn. Tentacruel, for instance, or a Whiscash for Earthquake.