With Pokémon Black 2 and White 2 on the way, commenter Daemon_Gildas has submitted a timely list of suggestions for freshening up a franchise that hasn't changed all that much in the past 16 years.
Dear Nintendo and/or Game Freak,
I'm going to give you a list that would make the Pokémon series kick SO MUCH ASS, and all because I just want to really love Pokémon again.
1. Let us customize out characters, at least to an extent. I'm fine with you guys sticking with sprites instead of 3D models, but give us some degree of customization. Different hats and hairstyles, clothes, skin color, eye color, and maybe even a few facial-hair options (nothing burly, just something a 17-year-old or younger might grow). Just make sure we can alter the appearance later, and maybe include a nice "Default" option for those who prefer the old experience.
2. Remove that God-forsaken EV and IV systems. EV'ing was a horrendous system to begin with, but when coupled with IV's, they just completely ruined the game for the casual player. In the late 90's, that was the beauty of Pokémon; anybody could feel competitive, if they played smart. Now, you just have to do ridiculous grinds, cheat, or don't even bother. It feels less like a game and more like work — something I just can't support.
3. Quit adding new Pokémon. Seriously, just stop it for right now. Focus on either giving each Pokémon a fully-3D model, or just adding a lot more frames of animation for each one. If you can handle that for all 450-ish Pokémon, great. If not, just do the first 151 — I'm sure a lot of players would give an "Anniversary Edition" a shot!
4. Remove Breeding. I'm sure this would be a controversial change, but it really has had a negative impact on the Trading community. "Legendary" Pokémon have become the only ones of any significant value, and being able to just breed Pokémon A) just seems really weird anyways, and B) robs you of that thrill of the hunt.
5. After beating the game, let us make our own Custom Gyms! Let us have X amount of Gym Trainers for our Gym, allowing us to equip them with any Pokémon we possess, and give us a variety of Themes, and let us lay down different types of blocks. It may sound like a strange feature to request, but I guarantee it would take off. At the least, let us customize our house (or perhaps import it from Animal Crossing somehow?)
6. Keep the Story to a minimum. Mewtwo was really cool because he broke out of a lab, and was like a "secret character". Some of the later games, though, just feel... well, stupid. Arceus is a Pokémon that apparently created the universe? Other Pokémon can control Time and Space, and even save the planet when the sun goes out? Just keep it simple and a little more believable. Pokémon's strong suit was always in that, as a kid, you felt like you could really go out into the woods and maybe see a Pokémon — the more extraordinary you get, the less "magic" it has.
7. Rather than any Pokémon being trapped in the pokeball you threw at it (which I'll admit, does make sense), why not also give us the option to use a single, custom Pokémon? Give us a variety of stickers and such to customize it, or even just use the appearance of those ones we really like (such as the surprisingly-memorable Master Ball).
8. Add some kind of Co-Op element. Even if you're not able to traverse the entire world together, I'm sure there could be some cool ideas. Perhaps a "Dungeon" that only allows you to use pre-set Pokémon, and requires both of you to work as a team. You can split up to solve puzzles, but the moment one of you enters combat, you're both thrust into the same battle. Whether it's for a special Badge, super-rare Pokémon, or even just for fun, I'm sure it would be a blast!
9. Give us a true reward for hitting those "Caught 'em All" benchmarks. For example, if you catch all 150 from the original games, only then should we be able to catch our own Mew. Continue doing Events, if you must, but allow us to catch our own truly rare Pokémon, don't just hand them to us at some arbitrary time or location.
10. Don't tell us who we are. The more back-story you add to our character, the more bogged-down it feels. Just say we're students of some kind who were relocated to aid our game's Professor with some research. Let us develop our Rival naturally, like in the Silver/Gold games. Similarly, rather than purchasing a "Red" or "Blue" version, why not tie the Pokémon that appear to who your starter Pokémon is?