Just going to make quick comments on a few things already mentioned.
Shiny Sableye & Eon Duo: Another neat thing about Shiny Sableye is the color of its gems. Normal Sableye only has red and blue gems, and being its a Gen III Pokemon come could say that's a reference to Ruby & Sapphire. Well Shiny Sableye has green and yellow gems, so not only does it add an Emerald reference but also a reference to the first gen of Pokemon.
Another neat Gen III Shiny trivia: The normally blue and red Latios and Latias turn cyan and yellow in their Shiny forms, respectively. Well in light color mixing, guess what color you need to mix with blue to get cyan and mix with red to get yellow? That's right, green. Yet another subtle Ruby, Sapphire, and Emerald reference. ;)
Gyms Puzzles: While I do like it when they show the Gym Leader being competent with having Pokemon that subverts the type advantage (such as Viola having a Surskit for those Fennekin trainers), from a Gym its not just the battles that intrigues me. For the most part the "dungeons" in Pokemon games are either natural structures (caves and forests) or buildings. And while they do their best to make some of these locations interesting (such as Unova's electrical Chargestone Cave, Kalos mirror full Reflection Cave), the "dungeons" I always look most forward to are the Gym puzzles because they're allowed to go beyond what is natural. If I had to pick some of my favorites it would be Goldrenrod Gym (if only because the floor structure was made to look like a Clefairy... even though they'd probably need to change it now (probably to a Jigglypuff, though as of now Munchlax is the only Normal-type that knows Metronome)), Blackthorn Gym because of the sheer obscurity of it (I don't know how in the world they got approval), many of the Sinnoh Gyms (its between a flower clock, smashing pile of tires with punching bags, messing with the plumbing, and math problems), most of Unova League Gyms (most favorite is BW's Mistralton for that cannon which shoots you into the wall and you comically slide down), and the Kalos League Gyms that took advantage of the new 3D graphics (like Cyllage Gym's rock climbing, Coumarine's climbing and swinging up & around a giant tree, and Olypmia's psychedelic maze in space). Gyms are really when the game designers can have some fun with the puzzles. Heck even Gyms which are just battling trainers like the first Gyms, Petalburg Gym, DP's Eterna Gym (combined with a game of hide and seek), HGSS's Cinnabar Gym, etc. are still interesting as they try to make the Gym surrounding look interesting and appropriate (my favorite of these is HGSS Violet Gym only because those who played GSC go in expecting the dollar sign layout only to find a platform... which then SHOOTS THEM UP to the ceiling where they find the gym hanging in the air. It's a nice update). Speaking of which I do like the updates they've down with the gyms in HGSS and ORAS, makes them fresh and new again and takes advantage of the better graphics of the times.
Nature Power In Space: I love that little attention to detail, I wonder if they just remembered Nature Power existed or did they go through all the moves and Abilities just to make sure there wouldn't be a problem with any (though now that makes me wonder if Earthquake would work when in space...). Connected to that they also have it change for other things you wouldn't immediately think it would:
1. While soaring in the air or on Sky Pillar they have Nature Power turn to Air Slash which is a nice touch too (sadly in XY when used in Sky Battles it was just Tri Attack). I kind of wished it also did Draco Meteor for Sky Pillar, but had they done that it being Draco Meteor in space probably wouldn't be that special.
2. The Terrain moves also changes what it becomes. Grassy Terrain is Energy Ball (like on normal Grass), Misty Terrain is Moonblast, and Electric Terrain is Thunderbolt. Yeah for attention to detail!
Character Details: Though people joked about how sitting on chairs and benches was the "best thing evar" when revealed, it does add a tiny bit. Crouching down to talk with small Pokemon and kids, sitting down, the way your character moves while skating, and then ORAS adding in more facial expressions, it gives much more character. Which they should, now that we've moved to 3D we can have such body quirks such as Wulfric smacking his belly, Tierno dancing, Furisode Girl spinning around in place (well actually that was kind of lazy, but at least it looked funny). I'm hoping as we go on they experiment more with adding more and more unqiue animations like maybe have Trainer Classes have their own animation and maybe even give the player a menu of animations they can do (sort of like Animal Crossing with the emotions).
Fairy Cute: While the Fairy Pokemon do have the cute thing down, I so also like how GF did their homework. For anyone who knows about a bit of ye olde Fairy lore, they were anything BUT cute. And this is reflected by us having some Fairy Pokemon which may seem odd at first until you know their origins. Mawile seems like an odd choice until you remember its based on a yokai which have fairy-like elements, Carbink is based on a fairy called a carbuncle, Mr. Mime's creepiness seem way off unless you know that's sort of how fairy were originally presented as (well, not like mimes, but they were humanoid-like with something creepy and off about them). Xerneas is the poster Fairy Legendary and its not cute, preferring to go with the more mystical side of Fairy. Also Fairy being weak to Steel is a nice reference to olde Fairy weakness to cold iron.
Different Ways to Battle: While some recent ways to battle haven't gone over so well like Sky Battles, I do like GF is trying to add some different ways to battle and even coming up with one of the best ones with Inverse Battles (which they seemed to have abandoned Sky Battles for if ORAS is anything to go by). Gen V's Triple Battles and Rotational Battles were also interesting additions (if underused) as well as the special rules used in Battle Facilities (and then we have Pokemon Contests). It sort of a proof of concept that the mechanics of the game aren't just good for single and double battles, rather they are a base which you can build upon, and that's a sign of good game design when it's so adaptable. Heck the type chart alone has been used in other Pokemon games when nothing else was.
Training To Be Super: I like how GF, despite people claiming otherwise, try to help with IV and EV training. When previously they tried pretending it was just how things naturally were and they couldn't be changed, over they years they've implemented tools in helping make it easier even to those who don't IV or EV train. Various items now have an effect while Breeding, Super Training puts EVs where you want them, and Legendaries now come with three stats at 31. There's of course still some improvements that can be made, but at this rate we should get those in time in some shape or form.
Name Game: Not only did the Kalos Route have names but they were in French which was very nice to see being the region is based on Paris. With the games needing to be translated in order to understand them, it's nice to have those places where you keep the language of the region's basis to help mold the feel of the origin. I also hope they keep that little detail in future games especially now that we're going all over the world.
Pokemon-Amie: For a franchise that encourages you to bond with your Pokemon, up till now it was pretty limited in how to do so. At best in HGSS you could interact with the Pokemon following you. Pokemon-Amie is what the franchise really needed. You can now really play, pet, and feed your Pokemon and they react appropriately. And they really put a lot of work into it, many Pokemon have spots they don't want you touching (or do if they don't like you. Did you know if you try petting an Espurr's/Meowstic's ear they back off... unless they don't like you. Remember, they get their devastating Psychic power from the secondary brains in their ears...) and their are some places on a Pokemon which you can't touch. And then there are some Pokemon you can't touch period (poor Slugma, even ghosts can be "pet" though its indicated your hand it going through them). But all this detail adds to the experience and makes it feel each Pokemon is unique (species wise, one Pikachu acts like another Pikachu. Sadly Natures don't play a part in Pokemon-Amie either) and helps you bond in different ways with your Pokemon who even gets some benefits for it (Critical hitting a Shiny Pokemon when you didn't mean to not withstanding).
I'll respond to more next post, though I should post some new things I like:
Has anyone mentioned player customization yet? So glad they finally added it, even though they skipped out on it for ORAS because nostalgia. And not only is it for clothes but also for hair and eye color! Now they still have much to improve on, but from what we got its a nice start, especially if you played as a girl who has twice as many clothing options than the boy, not counting the dresses. :P
And similar to that, though ORAS took away player customization they did give us Super Secret Bases where they let us build our own Gym! And to share them its easy as scanning a QR code or going on the PSS and tapping on someone's icon! :D