Emerald allowed you to play through the game by counteracting both Team Aqua and Team Magma's plans, which made the environmental balance themes much stronger, and did a decent job showing how Archie and Maxie both realized they were idiots for thinking more land/sea would solve the problem. By reverting back to Ruby and Sapphire's formula where you have to stop only one of the team's plans, it weakens the whole environmental balance that they were going for. You also see the other team functioning in ORAS, but barely ever hear from them within the story. Moreover, it makes this scene very pointless:
Why you may ask? Because what is the point of showing the lore of Hoenn's past if we're never going to actually see it? At least in Emerald, we were told how devastating it was to see Groudon and Kyogre diametrically opposing one another until Rayquaza balances them out. They could easily have re-interpreted that lore that we saw in Emerald by having both Primal Kyogre and Primal Groudon clash until Mega-Rayquaza ends the war. Not to mention, there's such a strange irony in how the cave paintings almost fit together as one puzzle, but yet get split off for stupid version exclusivity reasons.
I guess I get your point. Essentially it boils down to, it was a remake of RS, not Emerald. I know that's stupid, but it is what is.
Still salty over no Battle Frontier. Would've made ORAS one of the series best if it was included. Goddamnit.