It's a mixed bag, and some of my complaints are ones from the days of R/S/E. I want to do a full review on ORAS, but I need to plan that out. I'm not going to comment on the Delta Story, because I haven't gotten to it yet (I did beat the game once in a nuzlocke, but then went back to do another nuzlocke run with different rules).
Pros:
-Better graphics
The graphics definitely cater towards what the 3ds is capable of. Now, I do admit that I leave the 3D off, but otherwise, the graphics are amazing.
-Re-usable TMs
Like with Gen V and VI, you can re-use the TMs, so you don't have to worry about making the choice of "who am I going to teach that to, and how will I get another one once I use it?".
-The champ gets more involved with the story
I don't remember much of Ruby, but I really don't recall any interference being run by the champion. Like in X/Y, the champ just sort of left it up to the player to deal with a couple maniac teams. In ORAS, the champ gets much more involved, and you see him quite a lot.
-Secret bases
I honestly saw no point in secret bases in Ruby, and considered it a waste of money. There was no online play, so you were really the only one who ever saw your secret base. In ORAS, they introduced a "capture the flag" game with it, secret pals which can really help you out, and the ability to scan and share your own base using QR codes.
-The Sneak feature
This is, by far, one of my favorite features of ORAS. Granted, it doesn't always tell you everything about the pokemon (especially if you haven't encountered it a few times first), but these pokemon have a chance of having one or more perfect IVs, a higher level, a hidden ability, or an egg move.
-Pokemon Amie and Super Training
As a rule of thumb, I don't use Pokemon Amie when I nuzlocke because the more hearts your pokemon has, the more benefits you get (such as more exp in battle, or even the chance to shed a status condition without Shed Skin). For non-nuzlocke players (or nuzlockers who allow the use of Amie), it's a great feature.
Super Training is also excellent, because it's easier to understand and easier to use than prior EV training methods. Of course, for old-school EV trainers, hordes are still available.
Cons:
-There are still way too many HMs
Cut, Strength, Surf, Fly, Dive, Waterfall, Rock Smash...seven HMs, just like in R/S/E. And with the exception of Cut, you need ALL OF THEM to progress through the game. The move deleter isn't until Lilycove City, and in a game as long as Gen III and a world so large, it'll be quite some time before you can get rid of that crappy HM move.
-The amount of pokemon you can catch in one area is pathetically small
Hoenn is a tough region to nuzlocke, because it uses only Gen III pokemon until you get the National Dex (with the exception of a couple, such as marill, or locations such as the Safari Zone). Up until then, especially on later routes, there aren't many new pokemon to catch...and many of the "new" ones are water-types. Either way, there's barely any variety in what you can catch.
-The Safari Zone
I didn't bother with this in my copy of Ruby, but in ORAS, you need to have access to both bikes to get all of the items and access all of the areas in the safari zone. And, like above, the amount of pokemon you can get in the SZ is pathetic.
-The game feels much too easy
It's not just due to the exp share; gym leaders and gym trainers are easier to defeat for some reason. Brawly's gym once wiped out my entire team when I first played Ruby, and a couple of the trainers along the way really gave a smack-down on my pokemon. I went in with baited breath during my first run of AS (especially since I play with nuzlocke rules), and swept the entire gym with a Taillow which wasn't even over-leveled.
Neutral:
-Player customization
I'm also one who would have loved to see this come into ORAS, but let's be realistic; it's far easier to get money in X/Y than it is in ORAS, and you have no shortage of funds to drop on clothing. Yes, it'd be great to not look like every other player, but besides the money issue between the games, there was no customization option in the original R/S/E; so, I really had no expectations for this one.
-Hoenn is a HUGE region
I list this one under "neutral", because that's both a pro and a con. It's a long game, and the length makes it a true adventure, but sometimes, it just takes too long to get from one end of the map to the other.
-Freeflying on Latios/Latias
Probably one of the biggest letdowns, in my opinion, was this. Yes, you can fly around to mirage spots and battle legendaries, but I expected "freely travel the skies" to mean that I can stop at any point along a route, or at least have an option to go directly to a secret base (particularly my own) or a berry patch.
