Timed dialogue choices in Sakura Wars, which makes the visual novel half of the game more engaging. If the timer runs out, the player character remains silent. Sometimes, remaining silent is the right answer. Depends on the character you are talking to and the situation. These dialogue options can be spontaneous and affect gameplay a little bit. One timed dialogue that pops up during a battle forces you to recall the color a ribbon a girl was wearing earlier in the morning; failure to do so makes her demoralized and lowers her stats during the battle. In Sakura Wars V, you can angle your thumbstick to control the intensity of your response, which is a little difficult and stressful to do on a timer, trying not to whisper too low or shout in their face. Or shouting on purpose to be heard outside of the room. Depends upon the situation.
In Sakura Wars, you can mouse the cursor over a character's portrait to read their internal thoughts.
Sakura Wars 5: using the timed dialogue to simulate the protagonist's temptation. There is a moment where Gemini goes to another room, and you get a very long timed dialogue choice where your character is sitting at a table with Gemini's diary on it. If you don't immediately choose to read the diary, you're just sitting there seeing the timer bar fill and hearing the timer beep, for a full minute, and the option to end all and read her secrets is right there. Ofcourse you're going to read it (and get caught).
Final Fantasy VII: Wandering the overworld and seeing the huge Weapon mecha superbosses wandering around was pretty scary.
Final Fantasy IX: there is a scripted moment in the overworld in disc 1 where as you approach the world's most affluent city of Lindblum, you see other airships traveling to and fro that city on the overworld. It made the world feel more alive, like there were other people out there moving around besides your party, and also illustrated Lindblum as a trading center. Sadly it doesn't happen in regular gameplay, but I wish it had.
Animal Crossing: I like how if you spent enough money at Tom Nook's shop, he would close down the store for a day and then the next day you would come and see it completely revamped into a larger store with a different aesthetic, and there were several tiers of upgrades/revamps to look forward to seeing. I wish more games had done this with their stores.
Final Fantasy X: the game design incentivized you to use every character. Ie, switch in Auron to shatter the armor of heavily armored enemies. Switch in Tidus because he is fast enough to hit the wolves who would dodge otherwise. Switch in Wakka so he can use his ranged weapon to hit flying enemies that melee characters can't reach. Switch in Rikku and have her rip out the wires of mechs. Etc.
Zwei 1: you play as a duo of protagonists. The NPC dialogue and the flavor text you get from walking up to and interacting with objects (protagonist's internal thoughts) change depending upon which character you are controlling. Same thing with mousing over items in your inventory, the blurbs are different depending on which character you control.
Chronicles of Narnia: there is a level where you have to cross over a frozen lake, but if you use the heavier characters like Peter and Susan, they will break the ice and fall and drown. So you have to switch to the smaller and lighter Lucy and have her chart a safe path across first.
Final Fantasy XII: the geography of the environment changes depending upon the season. When you first visit the Giza Plains, it is dry and you can run across the riverbeds at any point, but when you return to it later it is wet and the river beds are filled up with water and you have to run across bridges at certain points. Also, different more dangerous mobs like alligators are present. It would be nice if more games had their environments change like this, ie a waterfall freezing in winter or snow piling up that you can traverse to access a new area.
The Last Remnant: dynamic final boss difficulty. In most JRPGs, if you are completionist, then the optional superboss will be the hardest and the story final boss will be underwhelming after that. But in TLR, the story final boss because more powerful the more side content you complete. If you beat everything then he will be harder than even the optional superbosses like The Fallen. Completing certain quests also gives the final boss new abilities because he acquired new Remnants.
Xenoblade Chronicles: Right as you set out from town on your journey at level 10, you find a big level 80 monster in the middle of the field that you cannot fight and must navigate around, and you are constantly looking over your shoulder for it. These monsters are placed throughout your journey. It's immersive, as many times in a video games it feels like the mobs you encounter were most conveniently just strong enough for you, whereas these guys at the top of the food chain do not care about your level and you cannot fight them at that point. It is satisfying to come back later and challenge them for real.
Final Fantasy XIV: the NPC party members will each resolve dungeon boss mechanics differently. In Dohn Mheg's final boss fight, there is a chasm that must be crossed. Thancred will leap across the chasm. Urianger will cast a teleportation spell to port to the other side. Ryne will slowly walk across the planks it trying to maintain her balance. Alisae will sprint across the planks to the other side. In Ktisis Hyperboreia, the first boss turns invisible. Alphinaud will look down for footprints in the snow, while Alisaie uses magic to blast the area, while Urianger teleports out at the last second, etc.
Trails series: sense that the world exists outside of the player. Every NPC's dialogue updates after time advances or an important plot event occurs. Every NPC has a storyline to follow. New newspapers come out every chapter or whenever a major event happens. Starting with the Cold Steel games, there is a calendar that gives you LotR-esque exact dates and months when things are happening.
Trails to Azure: There is a scene where a character tells you to observe a train passing by. The camera pans over the interiors of the three passenger cars populated by NPCs, and then the character asks you to recount how many passengers were on the train. Makes you pay more attention to what's going on.
Trails of Cold Steel 2, 3, Trails through Daybreak 1: you can find major antagonists (including the big bad in CS3 and Daybreak 1) as seemingly random background NPCs out in the world before they are introduced in the main story, let alone revealed as big bads.
► Trails Through Daybreak 1
Trails of Cold Steel 2, Trails Through Daybreak 2: The main menu screen depicts a scene depending on where your last save was at in the story.
Warframe: Missions objectives could dynamically change, with a rescue mission turning into an assassination mission mid way through. (Was eventually removed because players just wanted to farm the same mission type over and over again without it changing).
Starcraft 2 Legacy of the Void:
When you click to begin the final mission, the big bad immediately invades the mission briefing room, which was surprising and hyped him up as a threat.
The Banner Saga 2:
Juno enchants your map so you can see the huge radius of the darkness expanding as you advance across the world, which was threatening.
Final Fantasy XV: when night falls, you want to set up camp and go to bed. You get a scene of your characters eating together, and your total exp earned for that day is tallied up.
