Eh, it's all subjective I guess. Particularly in regards to the level design and UI. All of the areas in Hoenn are exactly the same as in the originals except for Granite Cave, Sky Pillar, Victory Road, Mauville, and Sea Mauville. And I'm pretty sure that we can agree that Sea Mauville and Sky Pillar are better than their original versions (especially since the new Sky Pillar took out that ******** with the cracked floor/Mach Bike). I'm fine with the UI on both games.
I think people are focusing on the graphics and story more because, like you said, Pokemon is usually ass when it comes to those 2 things and those were improved a lot, so they're the most noticeable changes.
Though I find it a little odd that Ruby/Sapphire/Emerald, which was made on and runs on older hardware, goes at nearly 60 fps while ORAS, which was made and runs on newer tech, is goin' at 30 fps.
But I think it's more than just the improved graphics/story that makes ORAS better than Ruby/Sapphire. ORAS has the updates to the game mechanics (move tutors, infinite use TMs, physical/special split, etc) that have come along since Gen III, it has new features like the DexNav and Soar, the availability of legendaries, and the Battle Resort/Battle Maison is better than the Battle Tower that R/S had. Little things like that. So compared to the original Ruby/Sapphire, ORAS seems a lot better.
How ORAS compares to Emerald though, idk. I never played Emerald.