This is just a small list I wrote about a year ago; I kept it tucked away in my Google Drive and never posted it anywhere. Today, while reorganizing my Drive, I stumbled upon it, and decided it might be fun to share.]
Beware of unmarked spoilers. [EDIT: December 12, 2015: Now with some TV Tropes links.]
- This is the only game (pair) in the franchise where your motivation for challenging the Elite Four is, at any point, not the comparatively self-centered goal of becoming the Champion for glory or ranking. Instead, you challenge them because it's the only option you have to reach and confront N, who at this point has issued a challenge where failure to win - and presumably, refusing to meet the challenge - means separation of Pokémon and humans the world over.
- Related to the above:
- The climax of the game's "Team X" storyline doesn't end before the 7th or 8th Gym badge, as it did in pretty much every other generation - instead, it's the final bosses, just after the Elite Four. This time, prior to the 8th badge is when the player learns of N's ultimate intention, and suddenly the heat is on to chase him to the Pokémon League, making the pursuit of the 8th badge much more purposeful.
- The game's experience system - which is only used in this generation - makes it harder to overlevel a team without seriously going out of one's way to level grind. As a result, many players arrive at the Elite Four with a team roughly equal in levels to the opponents'. This, I think, makes the final bosses much more exciting and challenging, with an increased reliance on good tactics even for veterans. (That Hydregion though.)
- The flow of events after defeating the Elite Four and marching forth to face N has a more-traditional JRPG feel, in my opinion. There's a lot of buildup, and it meets expectations instead of being an underwhelming letdown that's resolved in five minutes.
- Just after the "Pokémon League Under Siege" cutscene comes one of my favorite tracks in the game, "Carrying Out A Mission". It's right up there with "For the Savior" from Lufia 2 as far as heroic "we gotta do this" songs go - but unless you stand around for a bit, you only hear the first ten seconds, and it never plays again.
- The final boss feels like a final boss; that's not to say the Champions were never climactic or challenging or anything, but see my first bullet point - it was all friendly competition, and there was no danger or menace in those fights (with the possible slight exception of your Rival in Gen 1). This time, you're fighting a madman, and as far as you can tell, he's angry enough to kill you (he doesn't exactly try, but still).
- The ending cutscene is somewhat emotionally charged and has a beautiful track to go with it. You don't get the usual Hall of Fame bit, which may leave veterans feeling like they have unfinished business ...
- The game sets up a good ol' Checkov's Plot Trinket, which isn't made terribly obvious unless you play both versions of the game. I'm pretty sure this is the first time in the series that such a thing is done so early in the story, and without a huge neon sign that says "SUPER IMPORTANT THING HERE".
- Bianca, Cheren, Bianca's father, and N all get noticeable character development. This is well below (above? it's a negative thing after all, and in golf you score low ...) par for the course for most stories in general, but for a Pokémon game it's pretty nice, and it's done fairly well. Two of the related cutscenes even get pretty emotional pieces (and there are even more for N, delivered as flashbacks, in B2W2).
- The whole plot related to Team Plasma's purported goal legitimately calls into question the "slave or friend" debate on Pokémon, something that has been on the minds of many fans and Moral Guardians since the series' debut. It's not often that a kid-friendly game examines itself in this manner, and it provides plenty of food for thought. (N's possible backstory does too, though more in the form of Fridge Horror.)
- Despite the first bullet point, you can return to the Pokémon League after the credits and rematch the Elite Four - then properly challenge the Champion. He doesn't quite get the awesome battle theme other Champions have, but he makes up for it by having a pretty tough team at high levels (though keep in mind that, in story, N stomped this team flat), hot on the heels of Red's team. It takes a lot of level grinding to stand a chance if you didn't import a battle-hardened team from Gen 4, so it's a pretty meaningful battle for a lot of players.