I agree with a lot said on page 2. What I envision is a much more complex game that flows like the anime in a sense. Like you get to meet different NPCs and not just "battle a Team Rocket grunt, save their Pokemon and never see that NPC again" but ongoing interactions with different trainers.
On that note... RANDOM EVENTS!!!
After you play through a game once, every re-run is exactly the same other than the Pokemon team you assemble. I want to be able to interact in more complex ways than just "Click A on NPC. 'I love Pokemon. But I'm not too fond of scary looking ones'." I want to be able to ask them questions, either about themselves, the city/route they are in, etc. I kind of picture it as a mix between Skyrim and the Pokemon Anime. In Skyrim, each character has their own unique programmed things to do, and if you interact with them, that often changes. Maybe after you beat Youngster Joey you can talk to him and decide to work together to train and take on the first Gym Leader. And based on how much you interact he could either lose and stay behind, win and stay behind, or win and continue with you. And it would be up to the character.
And based on the NPCs that you build relationships with, some of them have their own motives, and you could run into some of them on the S.S. Anne, or in a deep cave. They wouldn't just be stationary in certain route, they would be roaming. And you would always have their phone numbers to call and see how they are doing, and it wouldn't just be about their Nidoran, or how they almost caught a Metapod, but they may have hatched an egg and want to share it with you, or beat a Gym Leader, or spotted Entei, or had a team Rocket member steal their Pokemon. Just tons and tons of random events so every time you play the game the possibilities are endless.
I could go on, but the reality that these things will never happen is too upsetting. Also loved the idea up there from a post from last April about diving into water to dodge attacks, or using Thunder Shock on the ground. That's where I see elements from the Anime working in.