Ooh, least favorite? Hmm...
This is gonna be a bit _long._
As the original Sapphire version is my favorite Pokemon game and game in general, I didn't like a lot of the changes in terms of item placement and such, but I'm not gonna harp on it solely for being different.
I personally thought that some of the remixes of the soundtrack didn't have much life to them, which I found really depressing. The Champion theme didn't sound nearly as epic as the original did, which was just a huge bummer.
I didn't mind the lack of trainer customization, but I would have loved it if they had the original outfits for the characters as options or unlockables.
I personally hated the fact that Wally has a Gallade now. The excuse of "they needed him to have a Pokemon that can Mega-Evolve" is not good enough, as Gardevoir also has one. I loved how the original game had Wally evolve his Ralts to a Gardevoir, which shows effort from a trainer. In ORAS, he could've just gotten a Dawn Stone and immediately shove it into Kirlia's face the second it evolved.
These last two are probably just me, but 1) I hate that they removed where I ALWAYS had my Secret Base (Route 119 right outside of Fortree City) and 2) I absolutely hated how most of the map transitions were just fades to black rather than scrolling into the map. I get that Pokemon maps usually works on Warp Points and Map Transitions, but this just personally bothered me. Like, really? A fade to black to go from Oldale to Route 103?