Well, Leaf only appears in FRLG if you answered "girl" to the
First Question. I feel that in HGSS, if you play as Lyra, Leaf appears at the top of Mt. Silver.
I know that, though who's to say both Red and Leaf can't exist? Here's another thing that I like: In the Gen V games the other playable character appearing in the Battle Subway if you choose to do tag battles. While they're just there to provide you a partner and don't talk, it's still nice to see them being used and even though we're not told anything about them in a way this does give them a bit of their own story. While we're going through the Unova League they're battling their way through the Battle Subway. Actually wasn't that what Twitch Plays Pokemon also concluded when you're forced to double battle Ingo and Emmet with the other playable character in BW2?
I've developed a bit of a reputation for harping on Black & White, but despite my frustrations with the story, I loved when they told it in little details. Like, going into N's room in the castle, or talking to the scientists that mention they can hack your PC effected me way more than any platitude N, Ghetsis, or Cheren said.
Adding in those pieces of character detail is always a nice touch. I don't remember them doing it much for Lyandre, but in XY I remember two cases of this. First is in
Perfume Parfum Palace is when you observe the portrait of the king it says just that, but after becoming Champion you go back and dialogue is added that you recognize the king as AZ. The second is in the Looker Missions. Now you may instinctual read the open book on Looker's desk, but did you do the same with the picture? During the Looker Mission observing the picture would tell you it shows Looker with a blue and red Pokemon (obviously Croagunk... though its kind of odd it doesn't say its a Croagunk since Croagunk are in the regional dex (not to mention at that time I was also carrying a Croagunk around with me in honor of Looker... and then I discovered what happened to Looker's Croagunk TT_TT)). Anyway once the Looker Missions are over and Emma is in charge of the Bureau the picture changes to that of the photo of you, Emma, Looker, and Xerosic eating at the restaurant. In ORAS though they did add some neat details for the Magma/Aqua boss and admins. The detail that stood out the most though was in Shelly's room where she has a picture of her, Archie, and a Jirachi. Hmm... that's something for the mystery thread.
FUN FACT: Speaking of neat little things about the Looker Mission, the tourist who speaks Japanese? Well in the Japanese version of the games she spoke English!
The menusprites! They've always looked so cute. X and Y improved them GREATLY so they resemble the actual Pokemon more closely. Wish they were still animated though. .cri
Also wouldn't hurt to give them a Shiny version as well. One of my favorite things they did with the menu sprites is using them for Super Training and having them hit the punching bag an when they finish they have the sprite flip around like it's destroying the punching bag, lol.
Speaking of that, I was super happy when I found out that the glass flutes were back with their original functions, having been useless in Generation V. Being able to save money on Awakenings and saving time having to switch out to heal confusion and infatuation is just nice to me. Hell, I had originally saved up a set of flutes to send forward to Generation V before I sadly learned that you couldn't send items forward.
I know that after seeing one had its function returned I made sure to pick up the rest. ;)
Now a new thing I like, hmm, have we mentioned
ending credits yet? My favorite ending credits are the ones which sort of retell your adventure with it ending you back at home. HGSS did it with having the sprites of the important NPCs come out and doing mostly funny things though it ends with your mom walking on screen, you walking up to her, and both of you going off screen. BW2 showed you your adventure going home visiting the important NPCs, most notably Burgh throwing you a parade in Castelia City! Finally ORAS showed us snapshots of our battles with the important NPCs showing the Pokemon we used to win the battle against them (as well as the bike ride with May ending us stopping in front of the small pool where we first met to have a post credit battle).