Does the PR Video Studio not count as a mini game?
It's more of an image editor than what we traditionally think is a game where there is a definite end goal. "Finishing editing an image is the end goal"! That's a subjective end goal, one where you decided to end the activity because you decided you were done. A definite end goal is when the game has a planned finished you're trying to reach on the programmed terms. For example Pokemon Contests, Musicals, and Pokeathlon the end goal is trying to show off your Pokemon best than your opponents to win first place, first place is a definite end goal. In Pokewoods Studio you're following vague instructions of a script to make the best movie you can to get high box office returns, the box office returns being another definite end goal (but one that you're not competing against anyone). PR Video Studio, decorating your Secret Base, making your League Card, playing with your Pokemon in Pokemon-Amie & its expies, etc. are all more side content/features which let's you play it as long as you feel like.
I really hope one day we will have the Z version we deserved ! There is so many things left in X&Y (I like the game mainly for the reasons Suspicious gave) and it could be better with a Z version on the Switch ! :)
The ghost girl, the South of France / Kalos, The Train Station, The Central / The desert, Haunted House, The tips (Sure it means something !), The cave near Route 22, AZ Floettte, Zygarde hunt, the lake in the east, All the rivers should be Surf-able, etc...
We're going to need to wait for their remakes which ain't gonna happen for another two consoles (since remakes go by consoles). Sinnoh is up next for the Switch remake, after that it's Unova (which should be interesting to see since you can't combine BW with BW2), and then its Kalos.
But let's quickly go over each of the mysterious you mentioned left behind for a second:
Ghost Girl: ... Does this need an explanation? The Pokemon series have had a number of ghost characters and rarely are they explained.
Most obvious example would be Sinnoh's Old Chateau which has ghosts of a butler and little girl you see float out of sight upon entering certain rooms never interacting (which may be a good thing considering what Pokemon Generations showed, poor Cheryl and Chansey). We don't know anything about them and aside from some loose theories made nothing is concretely confirmed (infact a note you find is more about how Charon used to live in the house and befriended a Rotom).
Unova is an interesting case as they actually do touch upon the ghost girl that appeared on Marvelous Bridge and revealing more of her story via encounters in the Strange House. I guess you could say this is a conclusion to her story, you find out what happened to her (she's a victim of a Darkrai and they were too late getting her a Lunar Wing) and as a bonus get the Lunar Wing to battle and catch a Cresselia.
XY obviously has the ghost girl who is waiting for someone (and also makes an appearance in ORAS). Speaking or ORAS, we got the ghost girl who appears just off screen when you're challenging Phoebe (some theories suggest she could be her grandmother's ghost who we can infer she's talking to in the post game on Mt. Pyre, but once again no concrete proof).
SM didn't have a ghost in the full game but in the demo they had a ghost of a girl who was waiting for her ship to come in, she tells the player she's afraid of boats and is nervous. She asks the player to see her off to ease her nerves, happy she can see her mom and dad again, and as you watch her about to pass through the gate a Machamp quickly walks by and she vanishes. If you talk with the lady behind the desk she says they're currently building the ferry.
And finally SwSh has the little girl in Hammerlocke who asks you to deliver a letter to a friend in Ballonlea who oddly turns out to be an old man. The man would say the girl who wrote the letter was a old friend, a girl who was sickly and when he moved he never heard from her again. When you go back to the spot the girl is gone but you can find a hidden item where she was standing: a Reaper Cloth (called Spirit World Cloth in Japan). In addition one of the man's granddaughters seems to be talking with something in the corner of the house (though considering Ballonlea is within a forest heavily populated by Fairy-types it could be anything from a ghost to a fey).
But overall my point is that, even if they do expand upon the ghost girl in XY I can't imagine it'll go anymore indepth than the ghost in Gen V. If I may dare speculate, it doesn't even seem SHE knows who she is looking for. Why approach the player if its then revealed he's not the one she's looking for. Wouldn't she know that just from a glance? Infact, she's a ghost, why is she waiting at all and not directly going to where they are? We know she's not stuck where she is as she later appears in ORAS. She's waiting for someone but doesn't seem to know who, and for all that is known said person may have passed on (and maybe she has something to do with the mysterious message on the back of the sign in Lumiose that says "I'm going to go for help. Wait in the usual place").
South of Kalos/Kiloude City: I wouldn't read too much into Kiloude City's description. All it's saying is that it's a city located in the south of Kalos. At most, if there was another game, they could maybe have added a few more cities/towns like they did in BW2 with the southwest of Unova (Aspertia City, Floccesy Town, & Virbank City).
The Central/The Desert: Not sure what you're talking about, do you mean the power plants in the Lumiose Badlands? Yeah, those are one of the locations where I think in Z version it was intended to be where you'd have an event encounter with Volcanion. There are several places like that such as that empty room in Reflection Cave where you find the Alakazamite (likely would be where Diancie would have an event) and the Chamber of Emptiness (likely would be where Hoopa would have an event).
Haunted House: I can only think of two places that match that description... and both don't really have anything more to add upon:
Scary House on Route 14: It's just meant to be a gag. You enter this creepy house where a guy tells a rather tame spooky story... then asks you for money. Maybe in Z version they could have different spooky stories but it's not meant to be an actual haunting. At most maybe the stories he tell have a nugget of truth to them if you follow the instructions given in them (maybe have one actually lead to a ghost encounter), but otherwise it was meant to be a silly little thing.
Lost Hotel on Route 15 & 16: It's not haunted, just abandoned. The moving trashcans are wild Pokemon who are looking for trash to eat or collect. It's nowadays just a hangout for Punks and oddly rollerskaters including a legendary rollerskater who teaches you the Cosmic Flip after getting all the other tricks. Like maybe in Z they could tell you about the history of the hotel but it'll only add lore at most.
The Tips: What tips? If you mean the message on the back of the Lumiose sign (the one that says "I'm going to go for help. Wait in the usual place"), honestly, I'd just leave it as is. Because in real life such messages are all over the place, someone left a message for someone else that only they'll ever understand. Did the person who was meant to get the message get it? Who knows. And who knows if the person that wrote it did what they said they were going to do. Or if they ever met up. Nearby you can find a guy asking if he's in the right place. Was he the guy meant to get the message or is it coincidence to show this sort of stuff happens all the time. While it doesn't add any lore exactly, it does make it feel like you're in a living world where there are things going on around you that you're just not a part of. It's no different from talking with an NPC after you battle them and they tell you something that's going on with them before moving on possibly forgetting about them.
Cave on Route 22/Chamber of Emptiness: Already discussed that above with The Central/The Desert.
AZ's Floette & Zygarde Hunt: Probably the biggest victim of no Z version. At least the Zygarde hunt was hastily moved into the Alola games even though it felt out of place there and had no bearing on the story which it probably would have in Z. As for AZ's Floette, huh, I'm curious how they would have given that out. Like, would AZ really give us the Floette he had been waiting 3,000 years to reconnect with? Or maybe this is another Floette, like AZ has secretly grown Eternal Flowers and to thank the player for helping him gives them another Floette he bonded with an Eternal Flower. Or is it maybe a non-canon thing, it would be an event distribution that just never came cause we jumped straight to Gen VII for the 20th Anniversary.
Lake In The East/Rivers To Surf: What lake to the east? You mean the lake that Anistar City overlooks? And I guess by surfable rivers you mean all the rivers running alongside the routes connected to it. Eh, sure, I guess would be neat to explore it if they add anything interesting and new hidden locations. But it's not like there was a big mystery concerning them, for Anistar the main mystery was with the sundial (and maybe Terminus Cave).