If I could change one thing... it would be the Gyms and the Elite Four. More specifically, how they respond to your challenge.
Let's take the Gyms first. At the moment, they appear to be pointless obstacle courses with random trainers strewn about. The Gym Leader is usually the most revered person in town, yet (s)he hardly does anything but standing there, and when you battle, the only difference from battling an ordinary trainer is a longer dialogue and a harder battle. And you get a badge afterwards. But apart from that, it is extremely unceremonial. Meet Gym Leader, battle Gym Leader, get badge, bye.
The gyms are dungeons or obstacle courses, that's fine, but those features seem so tacked on at the moment. It's like, "why would anybody spend their days in here?". In the Anime, gyms are training centers for people and Pokémon. The Gym Leaders tutor trainers, learn about their respective Pokémon type, and some gyms even have some community function (like Celadon Gym making perfume, for instance).
I was disappointed with the gyms in generations 2,3 and 4 (In generation I, I was too young, and everything was new and cool anyway). Luckily, Generation V breathed some fresh air into the concept. Striaton Gym is a battle-themed restaurant. Nacrene Gym is a museum AND a library, and you battle in its cellar. How cool is that? Driftveil Gym is a mine. However, the rest of the B/W Gyms were disappointing random mazes again.
BW2 had a few more interesting concepts, though. I fell deeply in love with Aspertia Gym, it really stunned me with its back-to-the-roots appearance. It has a classroom. A locker room. A little library. And - unique to the gyms so far - an actual battlefield. A large, flat, fenced-in area covered with sand. Arenas are marked in the sand, using actual marking equipment lying in the corner. There are even rakes to level the field again after every battle. There are grandstands. Floodlights. THIS is what a Gym should be. It is so clearly a place where young Trainers study with the guidance of a Gym Leader, where they learn to battle and where people can watch.
Another interesting Gym was Nimbasa gym. The strobe lights flickering back and forth. The music, subtle at first, then growing in intensity as the challenger proceeded through the gym. The shower of confetti, the lights going on, and the deafening music as Elesa appears. And, best of all, the spectators. This is what it should be like, when the best trainer in the city battles a travelling challenger. Music, lights, an actual crowd. Also, a field of battle. Your Pokémon clearly duke it out on the catwalk going through the gym. Your battle against the Gym leader is presented like a big event for the locals. People actually gather to watch the battle.
In future games, it would be cool with every gym having a puzzle, but also a clear battle arena you face the Gym leader on. The Gym shouldn't be a pure puzzle either, they could use some subtle hints indicating that more things went on in there than standing around, waiting for challengers. A locker room, a classroom, grandstands or doors you can't open. Just having a reception area where the "Champ-in-the-making-guy" stands would make the Gym seem so much more believeable. Also, the PWT has an audience. Contests have an audience. Why can't the Gyms have it too? A little cutscene before each Gym Leader battle, showing you facing each other in the arena, with some people watching the battle would be nice. It doesn't have to be Elesa's light and music show every time, but a little acknowledgement that this battle is important would be nice.
Reading the above, you can probably guess what my biggest beef with the Elite Four is. Gyms might be random obstacle courses with little going on, but they are pure festivals compared to the Elite Four. They reside in a building in the middle of absolutely nowhere. There is a small Pokémon Center/Mart, a few people hanging about, and then a big building with five mostly empty halls with powerful Trainers in them. Whoope-de-doo. At that point in the game, the player has achieved legendary status in the region. You've fought all the Gym Leaders, beaten the evil team of criminals threatening the security of the region/world(!), you've appeared on TV, in contests/musicals, heck, in BW2 you run a mall and are a movie star. And you've personally met and talked to almost every resident of the region. Now, you're up for your biggest challenge yet, you've made it through Victory Road, you battle the legendary quintet of the most powerful trainers in the region, you're trying for the very Hall of Fame. Yet nobody seems to care. The Elite Four Castle is such a desolate place I sometimes wonder if they are hiding from somebody. The gyms might be unceremonial, but the Elite Four represent a true anticlimax. If the PWT can manage to bring a crowd of spectators, a speaker and a pyrotechnics show for every battle, at least the Elite Four could send a camera man filming your challenge. Instead, you wander from empty room to empty room, battle a trainer you've never met before and won't meet again, and proceed to the next room. In the end, you face the familiar Champion, yet there are still just the two of you.
The worst offender so far in this regard is Pokémon Emerald. The Elite Four and the Champion reside in the most remote and featureless corner of the map. You've never met any of them before during your adventure (with the possible exception of Wallace, if you've played Ruby/Sapphire). Their castle is the plainest building in the region. It's a true borefest from beginning to end. And not even your mother show up to watch your challenge. At least Gabby and Ty should be there.
Yet beating them is a prerequisite for getting to the Battle Frontier, which gets all of these elements right. You're literally met with a trumpet fanfare upon arrival. There are hundreds of people there, discussing the various facilities. Crowds of people gather around the various buildings (which showcase some really cool architecture!) to discuss strategies. There is a records room you actually can enter (unlike the Hall of Fame, which really isn't what it's made out to be). A shop selling souvenirs. It's a living, breathing place, like an Olympic village. You have crowds cheering for you during challenges. Dozens of staff members guide you through it, suggesting that a lot of logistics is required to run the place. And nobody even mention the Elite Four, even though most of them would have beaten them to be eligible for the Frontier challenges. You defeating the Champion sure doesn't seem to be that special.
It's almost as bad in D/P too, where the Battle Zone is filled with interesting people and places, whereas the Elite Four castle is a random, lonely, empty building in the middle of nowhere.
I'd spruce up the Elite Four challenge the same way I'd do the gyms. Don't make their residence a castle, have it be a stadium, preferrably in or near a major city. Add some content to the surrounding area, such as hotels and resturants for people visiting, wanting to see the Hero duke it out against the most powerful trainers in the region. Have NPCs cheering for you, a crowd of spectators watching you battle. Instead of facing the Elite Four in separate rooms, let them enter the stadium in succession. You can go to a rest room between battles, but not leave the place unless defeated or victorious. And let the Hall of Fame be some sort of museum, where you're met with a little ceremony upon inclusion, and you could visit it later on instead of just accessing the data on a PC.
Tl;dr: I'd add some acknowledgement of your fame to the Pokémon League.
